DIVERSIDAD GENÉTICA/ESTADISITICA Y REDES DE CO-OCURRENCIA¶

Este tutorial utiliza un conjunto de datos de metabarcodificación reducido obtenido por C. Ribeiro y A. Lopes dos Santos. Este conjunto de datos se corresponde a la región 18S V4 amplificada en muestras clasificadas por citometría de flujo y secuenciada en una corrida Illumina 2*250 bp analizada con mothur.

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Las simbiosis entre algas eucariotas y cianobacterias fijadoras de nitrógeno han sido reconocidas en los últimos años como una fuente clave de nuevo nitrógeno en los océanos. Se investigo la composición de las pequeñas comunidades de eucariotas fotosintéticos asociados con cianobacterias fijadoras de nitrógeno en la bahía del Atlántico Sur de Brasil utilizando una combinación de citometría de flujo y secuenciación de alto rendimiento de dos genes: la región V4 de 18S rRNA y nifH. Se encontraron dos comunidades eucariotas distintas, una dominada por las mamielofíceas " Bathycoccus y Ostreococcus ", y otra dominada por una primnesiófita conocida por vivir en simbiosis con la cianobacteria fijadora de nitrógeno UCYN-A1. Entre las secuencias nifH, las de UCYN-A1 fueron las más abundantes, pero también se encontraron otros tres clados UCYN-A (A2, A3, A4). El análisis de redes confirmó la relación entre los clados A1 y A2 y sus hospedadores hipotéticos y señaló la posible asociación entre el nuevo clado A4 y Braarudosphaera bigelowii, que anteriormente se había considerado hospedador de A2.

In [ ]:
# Paquetes necesarios (Descomentar para instalar)
# Generamos 3 objetos con la lista de paquetes provenientes de los repositorios CRAN, Bioconductor, y GitHub

# cran_packages <- c("factoextra", conflicted", "readxl", "knitr", "qtl", "bookdown", "magrittr", "plyr", "ggplot2", "grid", "gridExtra", "tidyverse", "devtools", "dplyr", "pheatmap", "xtable", "kableExtra", "remotes", "Rtsne", "vegan", "RColorBrewer", "PoiClaClu", "gtools")
# bioc_packages <- c("airway", "phyloseq", "dada2", "DECIPHER", "phangorn", "ggpubr","DESeq2", "genefilter", "philr", "GenomeInfoDb", "microbiome")
# git_source <- c("zdk123/SpiecEasi", "twbattaglia/btools", "gmteunisse/Fantaxtic", "MadsAlbertsen/ampvis2", "opisthokonta/tsnemicrobiota")
# git_packages <- c("btools", "fantaxtic", "ampvis2", "tsnemicrobiota")


# Instalar paquetes
# Las instrucciones a continuación, primero búscan aquellos paquetes que no han sido instalados
# y los guarda en el objeto (".inst""; el punto al inicio indica que es un objeto oculto)
# para luego instalar estos paquetes según el repositorio fuente

## Instalar paquetes CRAN

#.inst <- cran_packages %in% installed.packages()
#if(any(!.inst)) {
#  install.packages(cran_packages[!.inst])
#}

## Instalar paquetes Bioconductor
### cargar la última versión de Bioconductor e instalar sus paquetes básicos

#if (!requireNamespace("BiocManager", quietly = TRUE))
#  install.packages("BiocManager")
#BiocManager::install()

### instalar paquetes

#.inst <- bioc_packages %in% installed.packages()
#if(any(!.inst)) {
#  BiocManager::install(bioc_packages[!.inst])
#}
  
## Instalar paquetes GitHub
  
#.inst <- git_source %in% installed.packages()
#if(any(!.inst)) {
#  devtools::install_github(git_source[!.inst])
#}

# Cargar paquetes en la actual sesión de R
#sapply(c(cran_packages, bioc_packages, git_packages), require, character.only = TRUE)

Phyloseq es un paquete de Bioconductor (Open Source Software For Bioinformatics) para la manipulación y análisis de datos metagenómicos generados por metodologías de secuenciación de alto rendimiento. Phyloseq es una herramienta para importar, guardar, analizar y visualizar éste tipo de datos después de haber sido procesados inicialmente, e.g., ensamblaje de novo, ASVs u OTUs (clustered), incluyendo otros importantes datos asociados (si están disponibles): tabla de observaciones asociadas a cada muestra (e.g., especie, localización geográfica, temperatura, etc.), conocida como sample data o metadata, árbol filogenético, e identificación taxonómica de cada OTU. La estructura del paquete phyloseq consiste en una serie de funciones de acceso y de proceso de objetos phyloseq. Estos objetos están compuestos de cuatro componentes que almacenan las cuentas de reads, la metadata, la taxonomía y el árbol filogenético. El paquete también provee una serie de herramientas para importar datos de otros programas. El siguiente diagrama muestra la estructura completa de phyloseq

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In [ ]:
# libreria
library("conflicted")
library("knitr")
library("qtl")
library("bookdown")
library("magrittr") 
library("plyr")
library("ggplot2") # esencial
library("grid")
library("gridExtra")
library("tidyverse")
library("devtools")
library("dplyr") # esencial
library("pheatmap")
library("xtable") 
library("kableExtra")
library("remotes")
library("Rtsne")
library("vegan")
library("RColorBrewer")
library("PoiClaClu")
library("gtools")
library("airway")
library("phyloseq") # esencial
library("dada2")
library("DECIPHER")
library("phangorn")
library("ggpubr")
library("DESeq2")
library("genefilter")
library("philr")
library("GenomeInfoDb")
library("microbiome")
library("btools")
library("tsnemicrobiota")
library("fantaxtic")
library("ampvis2")
library("tsnemicrobiota")
library("readxl") # esencial
library("SpiecEasi") # esencial
library("FactoMineR")
library("factoextra")
library("Matrix")
library("igraph")

Cambie tu directorio de trabajo al lugar donde se encuentran los archivos

Se necesitan tres tablas

OTU Taxonomía Muestras Se leen de un único archivo Excel en el que cada hoja contiene una de las tablas

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CONCEPTOS¶

En los análisis filogenéticos, una unidad taxonómica operativa (UTO), también conocida por la sigla OTU. Operational Taxonomic Unit—es una unidad de clasificación seleccionada por el investigador que la utiliza para individualizar a objetos de su estudio, ya sea una especie u otro taxón de cualquier categoría,una morfoespecie, una población, y hasta un individuo, y de este modo poder ordenarlos en una clasificación y en la construcción de un árbol filogenético, sin juzgar si se corresponden a una entidad biológica particular

In [ ]:
otu_mat<- read_excel("/Users/usuario/Documents/biologia_de_sistemas_posgrado/material_redes_coocurrencia_estadsitica/datacarbom/CARBOM data.xlsx", sheet = "OTU matrix")
print(otu_mat)

tax_mat<- read_excel("/Users/usuario/Documents/biologia_de_sistemas_posgrado/material_redes_coocurrencia_estadsitica/datacarbom/CARBOM data.xlsx", sheet = "Taxonomy table")
print(tax_mat)

samples_df <- read_excel("/Users/usuario/Documents/biologia_de_sistemas_posgrado/material_redes_coocurrencia_estadsitica/datacarbom/CARBOM data.xlsx", sheet = "Samples")
print(samples_df)
# A tibble: 287 x 56
   otu    X10n  X10p  X11n  X11p X120n X120p X121n X121p X122n X122p X125n X125p
   <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
 1 Otu0~ 13679  6292    42  2500 18850     5    43  7138  9432 10541     9  9772
 2 Otu0~    18  7134    38  9830    45 61420   182 23751    36    11  4535  3502
 3 Otu0~  9939  8983    31    13 24620    19    19    16 12502  3831  4621  2240
 4 Otu0~  3675  4234    24    22    11    16 32967    35     6    18  6908     5
 5 Otu0~     0     5     0     7     0     8     0    16 20166     0     0     2
 6 Otu0~     0     8     0     0     0     8     0     0     5     3     3     0
 7 Otu0~  4587   518     4   386  8775     5     6  1102 14336     0     0  3626
 8 Otu0~     1     8     2  4408     3    29     6 12355     0     0     0     0
 9 Otu0~   115   914     3   325     0   629     1   834     5     0  1354  2108
10 Otu0~   780     8 23810    12  3279     0    12     7  3027     0     2  4156
# i 277 more rows
# i 43 more variables: X126n <dbl>, X126p <dbl>, X127n <dbl>, X13n <dbl>,
#   X13p <dbl>, X140n <dbl>, X140p <dbl>, X141n <dbl>, X141p <dbl>,
#   X142n <dbl>, X142p <dbl>, X155n <dbl>, X155p <dbl>, X156n <dbl>,
#   X156p <dbl>, X157n <dbl>, X157p <dbl>, X15n <dbl>, X15p <dbl>, X165n <dbl>,
#   X165p <dbl>, X166n <dbl>, X166p <dbl>, X167n <dbl>, X167p <dbl>, X1n <dbl>,
#   X1p <dbl>, X2n <dbl>, X2p <dbl>, X3n <dbl>, X3p <dbl>, X5n <dbl>, ...
# A tibble: 287 x 8
   otu    Domain    Supergroup     Division    Class          Order Family Genus
   <chr>  <chr>     <chr>          <chr>       <chr>          <chr> <chr>  <chr>
 1 Otu001 Eukaryota Archaeplastida Chlorophyta Mamiellophyce~ Mami~ Bathy~ Ostr~
 2 Otu002 Eukaryota Hacrobia       Haptophyta  Prymnesiophyc~ Prym~ Braar~ UCYN~
 3 Otu003 Eukaryota Archaeplastida Chlorophyta Mamiellophyce~ Mami~ Bathy~ Bath~
 4 Otu004 Eukaryota Alveolata      Dinophyta   Dinophyceae    Dino~ Dinop~ Pror~
 5 Otu005 Eukaryota Stramenopiles  Ochrophyta  Bacillariophy~ Medi~ Medio~ Thal~
 6 Otu006 Eukaryota Stramenopiles  Ochrophyta  Bacillariophy~ Baci~ Bacil~ Pseu~
 7 Otu007 Eukaryota Stramenopiles  Ochrophyta  Pelagophyceae  Pela~ Pelag~ Pela~
 8 Otu008 Eukaryota Alveolata      Dinophyta   Dinophyceae    Dino~ Dinop~ Dino~
 9 Otu009 Eukaryota Hacrobia       Haptophyta  Prymnesiophyc~ Prym~ Chrys~ Chry~
10 Otu010 Eukaryota Opisthokonta   Metazoa     Craniata       Cran~ Crani~ Cran~
# i 277 more rows
# A tibble: 55 x 29
   sample fraction Select_18S_nifH total_18S total_16S total_nifH sample_number
   <chr>  <chr>    <chr>               <dbl>     <dbl>      <dbl> <chr>        
 1 X10n   Nano     Yes                 53230      8772         36 10           
 2 X10p   Pico     Yes                 47390      4448       6241 10           
 3 X11n   Nano     No                  24007      6193       3772 11           
 4 X11p   Pico     Yes                 31899        14      10201 11           
 5 X120n  Nano     Yes                 70455      5292         93 120          
 6 X120p  Pico     Yes                 76182     53272      23147 120          
 7 X121n  Nano     Yes                 52401      5958      26838 121          
 8 X121p  Pico     Yes                 71785     10993      23706 121          
 9 X122n  Nano     Yes                 78740     11730      15543 122          
10 X122p  Pico     Yes                 37364     11817      11045 122          
# i 45 more rows
# i 22 more variables: transect <dbl>, station <chr>, depth <dbl>,
#   latitude <dbl>, longitude <dbl>, picoeuks <dbl>, nanoeuks <dbl>,
#   bottom_depth <dbl>, level <chr>, transect_distance <dbl>, date <chr>,
#   time <chr>, phosphates <chr>, silicates <chr>, ammonia <chr>,
#   nitrates <chr>, nitrites <chr>, temperature <chr>, fluorescence <chr>,
#   salinity <chr>, sample_label <chr>, costa <chr>
In [ ]:
# Los objetos Phyloseq deben tener nombres de fila.

# definir los nombres de las filas de la columna otu

# tibble es una versión mejorada de la clase de objeto "data.frame".
# *Los nombres de las variables se preservar tal como se ingresaron
# *Los tibbles tienen un formato más limpio y fácil de leer que los data.frames
# *Las variables se imprimen en columnas separadas, lo que facilita la visualización de los datos

otu_mat <- otu_mat %>%
  tibble::column_to_rownames("otu")
print(otu_mat)
        X10n X10p  X11n X11p X120n X120p X121n X121p X122n X122p X125n X125p
Otu001 13679 6292    42 2500 18850     5    43  7138  9432 10541     9  9772
Otu002    18 7134    38 9830    45 61420   182 23751    36    11  4535  3502
Otu003  9939 8983    31   13 24620    19    19    16 12502  3831  4621  2240
Otu004  3675 4234    24   22    11    16 32967    35     6    18  6908     5
Otu005     0    5     0    7     0     8     0    16 20166     0     0     2
Otu006     0    8     0    0     0     8     0     0     5     3     3     0
Otu007  4587  518     4  386  8775     5     6  1102 14336     0     0  3626
Otu008     1    8     2 4408     3    29     6 12355     0     0     0     0
Otu009   115  914     3  325     0   629     1   834     5     0  1354  2108
Otu010   780    8 23810   12  3279     0    12     7  3027     0     2  4156
Otu011     0    3     2    2     0    13     5     5     4     7  3081    11
Otu012     0    0     0    6     0     0     0    16     3     0     0     0
Otu013  6321 2471     2    0    12     3     0     0     4 20272     0    15
Otu014     0   82     4 3304     1  1667     4  9233    13     3     0  2707
Otu015     0   12     0    3     7    25     1     6    10     0     4  2772
Otu016     1    0     0    9     5     0     0    14     0     0     0     0
Otu017     0    0     0    0     0     0     0     0    17     8     0     0
Otu018     1    0     9  911     0     0    15  2702     6     4   342  2217
Otu019     0    0    13    0     0     0    29     0     0     0     0     0
Otu020   425    0     1    0  1706     0  8447     1     0     0     0     0
Otu021     0    4     0    0     0    10     0     0     0     0     2     0
Otu022     0    0     0 4987     0     0     0     6    90     1     1   524
Otu023     4    0     1    0     0     3     0     0     0     0     0     0
Otu024     0    0     0    0     0     0     0     0     0     0     0    17
Otu025    69    0     0    0   290     0     0     0    21     0   118     2
Otu026     0    2     0    0     0     3     0     0     0     1     0     0
Otu027     6 2304     0    0     5     0     0     0    57     4     0 14529
Otu028    19  467     0  363    79     0     1   816     1     0   190     0
Otu029     0 1271     0    1     0     0  1794     1  1762   929   923     0
Otu030     0    5     0    0     0     4     0     0   155     0     1     0
Otu031     5 3945     0    0     0     0     0     7  2297     0     0     0
Otu032     0    8    10    0     0    16    19     5     0     3     0     4
Otu033     0    0     0    0     0     7     0     0     0     0     0     0
Otu034     0    0     0    0     0     0     0     0     0     0     3     0
Otu035     4    0     0    1     0     0     7     0     2     4  2499     1
Otu036     6    0     0    0    10     0     0     0     0     0     0     0
Otu037     0    0     0    5     0     0     0     7     0     0     0     0
Otu038     0    0     0  552     0     2     0  1518     3     0     0     0
Otu039   163    0     0    0   516     0   229     2     4     0     0     0
Otu040  1250    0     0    0     2     0     0    17  1660     0     0     0
Otu041     1    0     0    1     2     1     0     5     4     1     0     0
Otu042     3    0     0    0     7     0     0     0     0     0     0     0
Otu043  2818    0     0    0  8969     0     0     2     0     0     0     0
Otu044  1596    0     3    0     2     0     7     0     8     3     2  2484
Otu045     0    0     0    0     0     0     0     0     0     5     0     0
Otu046     0    1     0    0     0     0     0     0     0     0     0     0
Otu047     0    0     0  779     1     0     3  2460     0     1     0     0
Otu048     4    0     0    0     6     0     0     0     0     0     0     0
Otu049     0    0     0 2170     1     2     0  6430     3     0     0  1548
Otu050     2    0     0    0     4     0     0     0     0     0     0     0
Otu051    74   59     0  169   305     0     6   483     0     8    40    63
Otu052     3    0     0    0     4     0     0     0     0     0     0     0
Otu053  6651    0     0    0     3     0     0     0     0     0     0     0
Otu054     0    0     0    0     0     0     0     0     0     1     0     0
Otu055     0    0     0    0     0     2     0     0     0     0     0     0
Otu056     0 6374     1    3     0     7     0     0     0     0     1     0
Otu057     0    0     2    0     0     0     0     0     3  1123   812   596
Otu058     1    0     0    0     0     0     0     0     0     0     0     0
Otu059     0    0     0    2     0     1     0     9     0     1     0     3
Otu060     0  473     0    0     0  6699     0     0     0     0     0     0
Otu061     0    0     0    0     0     0     0     0     4     0     0     0
Otu062     0    0     0    0     0     2     0     1     0     0     0     0
Otu063     0    0     0    0     0     0     0     0  6382     0     0     5
Otu064     0    0     0    0     0     0     0     0     0     0     0     0
Otu065   164    0     0    0   729     0     0     1     0     0     0     0
Otu066     0   38     0    0     0   426     0     0    92     1     0   262
Otu067     0    0     0    0     0     0     0     0  1720     0     1     0
Otu068     0    0     1    0     0     0  1031     0     0     0     0     0
Otu069     0    0     0    0     0     0     0     3     1     0     0     0
Otu070     0    0     0    0     0     0     0     0     0   201     0     3
Otu071     0    0     0    0     0     1     0     0     0     0     0     0
Otu072     1    7     0    0     0    70     0     0     0     0     0    21
Otu073     0    0     0    0     0     0     0     0     0     0     0     0
Otu074     0    0     0    0     0     0     0     0     0     2     0   208
Otu075     0    0     0    1     4     0     0     0     4     0     0     1
Otu076     0    0     0    0     3     0     0     0     4     0     0     0
Otu077     0    1     0    0     0     0     0     0     0     0     0     0
Otu078     1  107     0  287     0  1254     1   759     0     0     0     0
Otu079     0    0     0    0     0     0     0     0  4154     0     0     0
Otu080     0    1     0    0     0     0     1     0     0     0     0     0
Otu081     0    0     0    0     0     0     0     0     0     0     0     0
Otu082     0    0     0    0     0     0     0     0     0     0     0     0
Otu083     0    0     0    1     0     0     0     2     0     0     0     0
Otu084     0    0     0    0     0     0     0     0     0     0     0     0
Otu085   263    7     0    0  1119   128     0     0     0     2     0     0
Otu086     0    0     0    0     0     0     1     0     0     0     0     0
Otu087     0    0     0    0     0     0     0     0     0     0     0     0
Otu088     0  244     0    0     0  2903     0     0     0     0     0     0
Otu089     0    0     1    0     0     0     0     0     0     0     0     0
Otu090     0    0     0    0     0     1     0     0     0     0     0     0
Otu091     0    0     0    0     0     0     0     0     0     0     0     0
Otu092     0    0     0    0     0     0     0     0     0     0     0     0
Otu093     0    0     0    1     0     0     0     1     0     0     0     0
Otu094     0    0     0  763     0     1     0  1820     0     0     0     0
Otu095     0    0     0    0     0     0   136     0     0     0   582     0
Otu096     0    0     0    0     0     0  2459     0     0     0     0     0
Otu097     0    0     0    0     0     0     0     0     1     0     0     0
Otu098     0    0     0    0     0     0     2     0     0     0     0     0
Otu099     0    0     0    0     0     0     2     0     0     0     0     0
Otu100     0    0     0    0     0     0     0     0     0     0     0     0
Otu101     0    0     0    0     0     0     0     0     0     0     0     0
Otu102     0    0     0    2     0     0     0     0     0     0     0     0
Otu103     0   34     0    0     0   236     0     0     0     0     0    59
Otu104     0    0     0    0     0     0     0     0     0     0     0   735
Otu105     0    0     0    0     0     0     0     0     0     0     0     0
Otu106     0    0     0    1     0     0     0     0     0     0     0     0
Otu107     0    0     1    0     0     0     0     0     0     0     0     0
Otu108     0    0     0    0     3     0     0     0     0     0     0     0
Otu109     0    0     0    0     0     0     0     0     0     0     0     0
Otu110     0    0     0    0     0     0     0     0     0     0     0     0
Otu111     0    0     0    0     0     0     0     0     0     0     0     0
Otu112     0    0     0    0     0     0     0     0     0     0     0     0
Otu113     0    0     0    0     0     0  1027     0     0     0     0     0
Otu114    88   38     1    0   104     0     0     0    36    35     0    51
Otu115     0    0     0    0     0     0  1530     0     0     0     0     0
Otu116     0    0     0    0     0     0     0     0     0     0     0     0
Otu117     0    0     0    0     0     0     0     2     0     0     0     0
Otu118     0    0     0    0     0     0     0     0     0     0     0     0
Otu119     0    0     0    0     0     0     0     0     0     0     8     0
Otu120    64   25     0    0   165     0     0     0    28    19    13     6
Otu121     0    0     0    1     0     0     0     0     0     0     0     0
Otu122     0 1109     0    0     0     2     0     0     0     0     0     0
Otu123   191   15     0    0    34     0     0     0    30    32     0    34
Otu124     0    0     0    0     0     0     0     0     0     0     0     0
Otu125     0    0     0    0     0     0     0     0     0     0     0     0
Otu126     0    0     0    0     0     0     0     0     0     0     0     0
Otu127     0    0     0    0     0     0     0     0     3     0     0   745
Otu128     0    0     0    0     0     0     0     0     0     0     0     0
Otu129     0    0     0    0     0     0     0     0     0     0     0     0
Otu130     0    0     0    0     0     0   887     0     0     0     0     0
Otu131     0    0     0    0     0     0     0     0     0     0     0     0
Otu132     0    0     0    0     0     0     0     0     1     0   209     1
Otu133     0    0     0    0     0     0     0     0     0     0     0     0
Otu134     0    0     0    0     0     0     0     0     0     0     0     0
Otu135   150    0     0    0   586     0     0     0     0     0     0     0
Otu136     0    0     0    0     0     1   732     0     0     0     0     0
Otu137     0    0     0    0     0     0     0     0     0     0     0     0
Otu138     0    0     0    0     0     0     0     0   424     0     0    49
Otu139     0    0     0    0     0     0     0     0     0     0     0     0
Otu140     0    0     0    0     0     0     0     0     0     0     0     0
Otu141    25    7     0    0    35     0     0     0    21    25     0     9
Otu142     0    0     0    0     0     0     0     0     0     0     0     0
Otu143     0    0     0    0     0     0     0     0     0     0     0     0
Otu144     0    0     0    0     0     0     0     0     0     0     0     0
Otu145     0    0     0    0     0     1     0     0     0     0     0     0
Otu146     0    0     0    0     0     0     0     0     0     0   264     0
Otu147     0    0     0    0     0     0     0     0     0     0     0     0
Otu148     0   48     0    0     0   520     0     0     0     0     0     0
Otu149     0    0     0    0     0     0     0     0     0     0     0     0
Otu150     0    0     0    0     0     0     0     0     0     0     0     0
Otu151     0    0     0    0     0     0     0     0     0     0     0     0
Otu152     0    0     1    0     0     0     0     0     2     0   458     0
Otu153     0    0     0    0     0     0   465     0     0     0     0     0
Otu154     0    0     0    0     0     0     0     0     0     0     0     0
Otu155     0    0     0    0     0     0     0     0     0     0     0     0
Otu156    16   15     0    0    34     0     0     0    16     6     8     0
Otu157     0    0     0    0     0     0     0     0     0     0     0     0
Otu158     0    0     0    0     0     0     0     0     0     0     0     0
Otu159     0    0     0    0     0     0     0     0     0     0     0     0
Otu160     0    0     0    0     0     0     0     0     0     0     0     0
Otu161     0    0     0    0     0     0     0     0     0     0     0     0
Otu162     0    0     0    0     0     0   323     0     0     0     0     0
Otu163     0    0     0    0     0     0     1     0     0     0   313     0
Otu164     0    1     0    0     0     0     0     0     0     0     0     0
Otu165     0    0     0    0     0     0     0     0     0     0     0     0
Otu166     0    0     0    0     0     0     0     0     1     0     0     0
Otu167     0    0     0    0     0     0     0     0     0     0     0     0
Otu168     1    0     0    0     0     0     0     0     0     0     0     0
Otu169     0    0     0    0     0     0     0     0     0     0     0     0
Otu170     0    0     0    0     0     0     0     0     0     0     0     0
Otu171     0    1     0    0     0     0     0     0     0     0     0     0
Otu172     0    0     0    0     0     0     0     0     0     0     0     0
Otu173     0    0     0    0     0     0     0     0     0   242     0     0
Otu174     0    0     0   25     0     7     0    42     0     0     0    13
Otu175     0    0     0    0     0     0     0     0     0     0     0     0
Otu176     0    1     0    0     0     0     0     0     0     0     0     0
Otu177     0    0     0    0     0     0     0     0     0     0     0     0
Otu178     0    0     0    0     0     0     0     0     0     0     0     0
Otu179     0    0     0    0     0     0     0     0     0     0     0     0
Otu180     0    0     0    0     0     0     0     0     0     0     0     0
Otu181     0    0     0    0     0     0     0     0     0     0    14     1
Otu182     3   17     0    0     5     0     0     0    29     3     9     0
Otu183     0    0     0    0     0     0     0     0     0     0     0     0
Otu184     0    0     0    0     0     0     0     0     0     0     0     0
Otu185     5    1     0    0    18     0     0     0     6     2     3     0
Otu186     0    0     0    0     0     0     0     0     0     0     0     0
Otu187     0    0     0    0     0     0     0     0     0     0     0     0
Otu188     7    5     0    0    16     0     0     0     4     2     3     0
Otu189     0    0     0    0     0     0     0     0     0     0    11     0
Otu190     0    0     0    0     0     0     0     0     0     0     0     0
Otu191     0    0     0    0     0     0     0     1     0     0     0     0
Otu192     0    0     0    0     0     0     0     0     0     0     0     0
Otu193     0    0     0    0     0     0     0     0     0     0     0     0
Otu194     0    0     0    0     0     0     0     0     0     0     0     0
Otu195     0    0     0    0     0     0     0     0     0     0     0     0
Otu196     0    0     0    0     0     0     0     0   118     0     0     0
Otu197     0    0     0    0     0     0     0     0     0     0     0     0
Otu198     0    0     0    0     0     0     0     0     0     0     0     0
Otu199     0    0     0   24     0     0     0    74     0     0     0     7
Otu200     0    0     0    0     0     0     0     0     0     0     0     0
Otu201     0    0     0    0     0     0     0     0     0     0     0     0
Otu202     0    0     0    0     0     0     0     0     0     0     0     0
Otu203     0    0     0    0     0     0     0     0     0     0     0     0
Otu204     0    0     0    0     0     0     0     0     0     0     0     0
Otu205     0    0     0    0     0     0     0     0     0     0     0     0
Otu206     0    0     0    0     0     0     0     0     0     0    12     0
Otu207     0    0     0    0     0     0     0     0     0     0     0     0
Otu208     0    0     0    0     0     0     0     0     0     0     0     0
Otu209     7    0     0    0    13     0     0     0     0     0     0     0
Otu210     3    3     0    0     5     0     0     0     4     3     0     1
Otu211     0    0     0    0     0     0     0     0     0     0     1     0
Otu212     0    0     0    0     0     0     0     0     0     0     0     0
Otu213     0    0     0    0     0     0     0     0     0     0     0     0
Otu214     0    0     0    0     0     0     0     0     0     0     0     0
Otu215     0    0     0    0     0     0     0     0     0     0     0     0
Otu216     0    0     0    0     0     0     0     0     0     0     0     0
Otu217     0    0     0    0     0     0     0     0     0     0     0     0
Otu218     0    0     0   12     0     0     0    33     0     0     0     0
Otu219     5    3     0    0     2     0     0     0     0     0     4     0
Otu220     0    0     0    0     0     0     0     0     0     0     0     0
Otu221     0    0     0    0     0     0     0     0     0     0     0     0
Otu222     4    3     0    0     0     0     0     0     2     0     0     1
Otu223     0    0     0    0     0     0     0     0     0     0    13     0
Otu224     0    0     0    0     0     0     0     0     0     0     0     0
Otu225     0    0     0    0     0     0     0     0     0     0     0     0
Otu226     0    0     0    0     0     0     0     0     0     0     0     0
Otu227     0    3     0    0     5     0     0     0     4     0     3     0
Otu228     0    2     0    0     1     0     0     0     0     0     0     3
Otu229     0    0     0    0     0     0     0     0     0     0     0    47
Otu230     2    0     0    0     2     0     0     0     2     1     0     0
Otu231     0    0     0    0     0     0     0     0     0     0     0     0
Otu232     0    0     0    0     0     0     0     0     0     0     0     0
Otu233     0    0     0    0     0     0     0     0     0     0     0     0
Otu234     0    1     0    0     4     0     0     0     2     0     0     0
Otu235     0    0     0    0     0     0     0     0     0     0     0     0
Otu236     0    0     0    3     0     0     0    14     0     0     0     0
Otu237     4    0     0    0     7     0     0     0     0     0     0     0
Otu238     0    0     0    0     0     0     0     0     0     4     0     0
Otu239     0   32     0    0     0     0     0     0     0     0     0     0
Otu240     0   32     0    0     0     0     0     0     0     0     0     0
Otu241     0    0     0    0     0     0     0     0     0     0     0     0
Otu242     0    2     0    0     3     0     0     0     0     0     0     0
Otu243     0    0     0    0     0     0     0     0     0     0     0     0
Otu244     0    0     0    0     0     0     0     0     0     0     0     0
Otu245     0    0     0    0     3     0     0     0     0     0     0     0
Otu246     0    0     0    0     0     0     0     0     0     0     0     0
Otu247     0    0     0    0     0    25     0     0     0     0     0     0
Otu248     0    0     0    0     0     0     0     0     0     0     0     0
Otu249     0    0     0    0    12     0     0     0     0     0     0     0
Otu250     0    0     0    0     0     0     0     0     0     0     0     0
Otu251     1    1     0    0     0     0     0     0     0     0     0     1
Otu252     0    0     0    0     0     0     0     0     0     0     0     0
Otu253     0    0     0    0    21     0     0     0     0     0     0     0
Otu254     1    0     0    0     0     0     0     0     1     1     0     0
Otu255     0    0     0    0     0     0     0     0     0     0     0     0
Otu256     0    0     0    0     0     0     0     0     0     0     0     0
Otu257     0    0     0    4     0     0     0     6     0     0     0     0
Otu258     0    0     0    0     0     0     0     0     0     0     0     0
Otu259     0    0     0    0     0     0     0     0     1     0     0     0
Otu260     0    0     0    0     0     0     0     0     0     0     0     0
Otu261     0    0     0    0     0     0     0     0     0     0     0     0
Otu262     0    0     0    0     0     0     0     0     0     0     0     0
Otu263     0    0     0    0     0     0     0     0     0     0     0     0
Otu264     0    0     0    0     0     0     0     0     0     0     0     0
Otu265     0    0     0    3     0     0     0    10     0     0     0     4
Otu266     0    0     0    0     0     0     0     0     0     0     0     0
Otu267     0    0     0    0     0     0     0     0     0     0     0     0
Otu268     0    0     0    0     2     0     0     0     1     0     1     0
Otu269     0    0     0    0     0     0     0     0     0     0     0     0
Otu270     0    0     0    0     0     0     0     1     0     0     0     0
Otu271     0    0     0    0     0     0     0     0     0     0     0     0
Otu272     3    0     0    0     0     0     0     0     0     0     0     4
Otu273     0    0     0    0     0     0     0     0     0     0     0     4
Otu274     0    0     0    0     0     0     0     0     0     0     0     0
Otu275     0    0     0    0     0     0     0     0     0     0     0     0
Otu276     0    0     0    0     0     0     0     0     0     0     0     0
Otu277     0    0     0    0     0     0     0     7     0     0     0     0
Otu278     0    0     0    0     0     0     0     0     0     0     0     0
Otu279     0    0     0    0     0     0     0     0     0     0     0     0
Otu280     0    0     0    0     0     0     0     0     0     0     0     0
Otu281     0    0     0    0     0     0     0     0     0     0     0     0
Otu282     0    0     0    0     0     0     0     9     0     0     0     0
Otu283     0    1     0    0     0     0     0     0     0     0     0     0
Otu284     0    0     0    0     0     0     0     0     0     0     0     0
Otu285     0    0     0    0     0     0     0     0     0     0     0     0
Otu286     0    0     0    0     0     0     0     0     0     0     0     0
Otu287     0    0     0    0     0     0     0     0     0     0     0     0
       X126n X126p X127n  X13n  X13p X140n X140p X141n X141p X142n X142p X155n
Otu001  1388     7 31538    38  2338    23     9  1358    36    42     0    43
Otu002 11018  5473    26 14411    38 19018    12  3080    20    37  6855    56
Otu003  9924  4052  9292    18     0    37     7  3680 14740 57440  5712    47
Otu004    16  8702    24    11 37717     0    25  4196     4     9     5    31
Otu005     5     8     2    16     0    13     0     0     0     0     5     0
Otu006     0     9     0     5     4     0     0     3     0     0    10     0
Otu007    51     0     6    12     0    10     0   395  3488     8     0  7815
Otu008     0     9     3  1588     0     6     3     3     4    12 27737    10
Otu009  1117    67     0  2010  1897 11227     1     3     5     1     1   203
Otu010     0     0    18     0     0     0     0     0     6     0     0    22
Otu011     4  6804     0     3    11     0     5     0     9     0     4     1
Otu012     0     0     0    17     0     6     0     0     0     0     0     0
Otu013     9     0     5     0    11     0    14     0     5     4     1     0
Otu014     0     0     3  4806     9     3     5     0     2     0     0     2
Otu015     1     3     0     2     0    10    13  8052     7    23 28084    15
Otu016  2654     0     0     6     1     1     0     0     0     1     0     0
Otu017     0     0     0    17    24    48 35210     4     4     7     3     7
Otu018   606     0    13  3846     4     6  8513     1     2     5     3    21
Otu019     0     0    11     0     0     5     4     0     0     2     3 32076
Otu020     0    26     0     0  3490     0  2620     0     0     0     0     0
Otu021     0     4     0     0     0     0     0     4     0     0     8     0
Otu022     0   467     0     4     8  6198     0     1     3     0     2     0
Otu023  3351     3     0  3910     1     2     3     0  2682     4     4     0
Otu024     0     0     0     0     0     2     1     0 28004     0     4     6
Otu025     9   513     2     0     0     2     0     0  5182 10962     0     8
Otu026     0     0     0     0     0     0     0     0     2     0     3     0
Otu027  9597     2     6     0     0     0     0     0    12     7     0     0
Otu028    10     1     0   140     0     0     0     0     1    13  1040     0
Otu029   764     1     5     2    24    10    13  8017     7     5  1595     7
Otu030     0     5     0     0     0     0     0     1     0     0     5     0
Otu031     0     0     0     0  4012     0     0     0     0     0     0     0
Otu032   676    21 17450     0     0     0     0     0     1     1    17    16
Otu033     0     0     0     0     0     0     0     0     0     0     1     0
Otu034     0     0     0     0     0     0     0     9     0     0     0     0
Otu035  4357     1    12  1231     0     0     0     0     0     1     0     6
Otu036     0     0     0     0     0     0     0     0     0     4     0     0
Otu037     0     0     0     0     0     0     0     0     0     0     0     0
Otu038   654   877     1  6512     0     0     0     0     0     0     0     0
Otu039     0     0     0     7  2262 10132     0     0     0     0     0     0
Otu040     1     0     0     2  1132     0     0     0     1     0     4     0
Otu041  3724     0     1   646     0     0     0     0     0     0     0     0
Otu042     4     0     0     0     0     0     0     0     1     3     0     0
Otu043     0     0     0     1     0     0     0     0     0     0     0     0
Otu044  1815     0  1355     0     0     0     0     0     1     2     0  4018
Otu045     0     0     0     0     4     0     3     0     0     0     0     0
Otu046     0     0     0     0     0     0     0     2     0     0     0     0
Otu047   561     0     0  1192     0     0     0     0     0     0     0     0
Otu048     2     0     0     0     0     1     1     0     0 10261     0     0
Otu049     1     0     0     3     0     0     0     0     0     0     0     0
Otu050  2401     0     0     0     0     1     3     0     0  3348     0   127
Otu051    69     0    50     0    15  1347    62     0   344     0    10  4522
Otu052     1     0     0     0     0     0     0     0     0     0     0     0
Otu053     4     0     0     0     0     0     0     0     0     4  2333     0
Otu054     0     0     0     0     0     0     0     0     0     0     0     0
Otu055     0     1     0     0     0     0     0     0     0     0     4     0
Otu056     0     0     0     0     0     0     0     0     0     0     3     0
Otu057     0     0   421     0     1     0     0     0     0     1     0  5063
Otu058     0     0     0     3     1     0     0     0  5033     0     0     0
Otu059     0     1     2     0     0     0     0     0     0     0     0     0
Otu060     0     0     0     0     0     0     0     0     0     0     1     0
Otu061     0     0     0     1     0     1     0     0     0     0     0     0
Otu062     0     0     0     0     0     0     0     0     0     0     0     0
Otu063     0     0     0     0     0     3     0     0     0     0     0     0
Otu064     0     0     0     0     2     0     3     0     0     0     0     0
Otu065     1     0     0     0     0     0     0     0     2     1     0     0
Otu066    91     0     0    58     0     0     1   271   392  1076  1700     0
Otu067     0    89     0     3     0     0     0     1     0     0     1     0
Otu068     0     0     0     0  2957     0     1     0     0     0     0     0
Otu069     0     0     0  2691     0     0     0     0     0     0     0     0
Otu070     0     0     0     0     0     0     1     0  3115     0     0     1
Otu071     0     2     0     0     0     0     0     0     0     0     0     0
Otu072    20     0     0    43    67     0     0     0     0     0     0     0
Otu073     0     0     0     0     0     1     0     0     0     3  4613     1
Otu074     0     0     0     0    11     0    23    22    33     0     0    11
Otu075  3689     0     3     0     0     0     0     0     0     0     0     0
Otu076  4321     0     0     0     0     0     0     0     0     7     0     0
Otu077     0     3     0     0     0     0     0     0     1     0  4278     0
Otu078     0     0     0   373     0     0     0     0     0     0     0     0
Otu079     1     0     0     0     0     4     0     0     0     0     0     0
Otu080     0     0     0     0  3112     0     5     0     0     0     0     0
Otu081     0     0     0     0     0     0     0     0     0     0     0     0
Otu082     0     0     0     0     0     0     0     0     0     0     0     0
Otu083     0     0     0     0     0     0     0     0     0     0     0     0
Otu084     0     0     0     0     0     2     0     0     0     3  3716     0
Otu085     1     0     0     0     2     0     0     0     0     0     0     0
Otu086     0     0     0     0     0     0     0     0     0     0     0     1
Otu087     0     0     0     0     0     0     0     0     0     0     0     0
Otu088     0     0     0     0     0     0     0     0     0     0     0     0
Otu089     0     0     0     0     0     0     0     0     0     0     0     0
Otu090     0     1     0     0     0     0     0     0     0     0     1     0
Otu091     0     2     0     0     0     0     0     1     0     0     0     0
Otu092     0     0     0     0     0     0     0     0     0     0     0     1
Otu093     0     0     0     0     0     0     0     0     0     0     0     0
Otu094     0     0     0     0     0     0     0     0     0     0     0     0
Otu095     0     0     0     0     0     0     0     0     0     0     0     4
Otu096     0     0     0     0     0     0     0     0     0     0     0     0
Otu097     0     0     0     2    46     3     0     0     0     0     0     0
Otu098     0     0     0     0     0     0     0     0     0     0     0     0
Otu099     0    35     0     0     0     0     0     0     0     0     0     0
Otu100     0     0     0     0     0     0     0     0     0     0     0     0
Otu101     0     0     0     0     0     0     0     0     0     0     0     0
Otu102     0     0     0     0     0     0     0     0     0     0     0     0
Otu103    54     0     0   138   282     0     0     0     0     0     1     0
Otu104     0    20     0   721     0     0     0     0     0     0     0     0
Otu105     0   465     0     0     0     0     0     0     0     1  1479     0
Otu106     0     0     0     0     0     0     0     0     0     0     0     0
Otu107     0     0     0     0     0     0     0     0     0     0     0     0
Otu108     0     0     0     0     0     0     0     0     0     0     0     0
Otu109     0     0     0     0     0     0     0     0     0     0     0     0
Otu110     0     0     1     0     0     0     0     0     0     0     0     0
Otu111     0     0     0     0     0     0     0     0     0     0     0     0
Otu112     0     0     0   460     0     0     0   956     2     5     0     0
Otu113     0     0     1     0     0     0     0     0     0     0     0     0
Otu114     0     0   103     1     0     0     0     5     0     0     0     0
Otu115     0     0     0     1     0     0     0     0     0     0     0     0
Otu116     0     0     0     0     0     0     0     1     0     0     0     0
Otu117     0     0     0     0     0     0     0     0     0     0     0     0
Otu118   155     0     0     0     0     0     0     0     0     0     0     1
Otu119     0     0     0   892     0     3     0     2     0     0     0     0
Otu120    21     3    32     0     0     0     0     0    23   116     6     0
Otu121     0     0     0     0     0     0     0     0     0     0     0     0
Otu122     0     0     0     0     0     0     0     0     0     0     0     0
Otu123     0     0   123     0     0     0     0     2     0     0     0     1
Otu124     1     0     0     0     0     0     0     0     0  1061     0     0
Otu125     0     0     0     0     0     0     0     0     0     0     0     0
Otu126     0     0     0     0     0     0     0     0     0     0     0     0
Otu127     0     0     0     0   118     0     0     0     0     0     0     0
Otu128    53     0     0     0     0     0     0     0     0     0     0     0
Otu129     0     0     0     0     0     0     0     0     0     0     0     0
Otu130     0     0     0     1     0     0     0     0     0     0     0     0
Otu131     0     0     0     0     0     0     0     0     0     0     0     0
Otu132     0   586     0     0     0     0     0     0     0     0     0     0
Otu133     0     0     0     0     0     0     0     0   753     0     0     0
Otu134   746     0     0     0     0     0     0     0     0     2     0     0
Otu135     0     0     0     0     0     0     0     0     0     0     0     0
Otu136     0     0     0     0     0     0     0     0     0     0     0     0
Otu137     0     0     0     0     0     0     0     0     0     0     0     0
Otu138     0     0     0     0     0     0     0     0     0     0     0     0
Otu139     0     0     0     0     0     0     0     0     0     0     0     0
Otu140     0     0     0     0     0     0     0     0     0     0     0     0
Otu141     0     0    51     0     0     0     0     2     0     0     0     0
Otu142     0     0     0     0     0     0     0     0     0     0     0     0
Otu143     0     0     0     0     0     0     0     0     0     0     0     0
Otu144     0   675     0     0     0     0     0     0     0     0     0     0
Otu145     0   634     0     0     0     0     0     0     0     0     0     0
Otu146     0     0     0     0     0     0     0     0     0     0     0     0
Otu147     0     0     0     0     0     0     0     0     0     0     0     0
Otu148     0     0     0     0     0     0     0     0     0     0     0     0
Otu149     0     0     0     0     0     0     0     0     0     0     0     0
Otu150     0     0     0     0     0     0     0     0     0   485     0     0
Otu151   470     0     0     0     0     0     0     0     0     0     0     0
Otu152     0     0     0     0     0     0     0     0     0     0     0     1
Otu153     0     0     0     0     0     0     0     0     0     0     0     0
Otu154     0     0     0     0     0     0     0     0     0     0     0     0
Otu155   459     0     0     0     0     0     0     0     0     0     0     0
Otu156    11     0    10     0     0     0     0     2    18    95    12     0
Otu157   437     0     0     0     0     0     0     0     0     1     0     0
Otu158     0     0     0     0     0     0     0     0     0     0     0     0
Otu159     0     0     0     0     0     0     0     0     0     0     0     0
Otu160    51     0     0     0     0     0     0     0     0     0    77     0
Otu161    20     0     0     0     0     0     0     0     0     0     0     0
Otu162     0     0     0     0     0     0     0     0     0     0     0     0
Otu163     0     0     0     0     0     0     0     0     0     0     0     0
Otu164     0     0     0     0     0     0     0     0     0     0   310     0
Otu165     0     0     0     0     0     0     0     0     0     0     0     0
Otu166     0   272     0     0     0     0     0     0     0     0     0     0
Otu167     0     0     0     0     0     0     0     0     0     0     0     0
Otu168     0     0     0     0     0     0     0     0     0     0     0     0
Otu169     9     0     0     0     0     0     0     0     0     0     0     0
Otu170     0     0     0     0     0     0     0     0     0     0     0     0
Otu171     0   256     0     0     0     0     0     0     0     0     0     0
Otu172     0     0     0     0     0     0     0     0     0     0     0     0
Otu173     0     0     0     0     0     0     0     0     0     0     0     0
Otu174     0     0     0    22     0     0     0     0     0     0     0     0
Otu175     0     0     0     0     0     0     0     0     0     0     0     0
Otu176     0     0     0     0     0     0     0     0     0     0     0     0
Otu177     0     0     0     0     0     0     0     0     0     0     0     0
Otu178     0     0     0     0     0     0     0     0     0     0     0     0
Otu179     0     0     0     0     0     0     0     0     0     0     0     0
Otu180     0     0     0     0     0     0     0     0     0     0     0     0
Otu181     0    16     0     0     0     0     0     0     0     0     0     0
Otu182     8     7     3     0     0     0     0     3     4    17    11     0
Otu183     0    17     0     0     0     0     0     0     0     0     0     0
Otu184     0     0     0     0     0     0     0     0     0     0     0     0
Otu185     6     4     4     0     0     0     0     1     8    30     5     0
Otu186     0     0     0     0     0     0     0     0     0     0     0     0
Otu187    10     0     0     0     0     0     0     0     0     0     0     0
Otu188     6     3     3     0     0     0     0     2     5    19     4     0
Otu189     0    15     0     0     0     0     0     0     0     0     0     0
Otu190     0     0     0     0     0     0     0     0     0     0     0     0
Otu191     0     0     0    87     0     0     0     0     0     0     0     0
Otu192     0     0     0     0     0     0     0     0   133     0     0     0
Otu193     0     0     0     0     0     0     0     0     0     0     0     0
Otu194     0     0     0     0     0     0     0     0     0     0     0     0
Otu195     0     0     0     0     0     0     0     0     0     0     0     0
Otu196     0     0     0     0     0     1     0     0     0     0     0     0
Otu197     0   114     0     0     0     0     0     0     0     0     0     0
Otu198     0     0     0     0     0     0     0     0     0     0     0     0
Otu199     0     0     0     0     0     0     0     0     0     0     0     0
Otu200     0     1     0     0     0     0     0     0     0     0     0     0
Otu201     0    29     0     0     0     0     0     0     0     0    72     0
Otu202     0     0     0     0     0     0     0     0     0     0     0     0
Otu203     0     0     0     0     0     0     0     0     0     0     0     0
Otu204     0     0     0     0     0     0     0     0     0     0     0     0
Otu205     0     0     0     0     0     0     0     0     0     0     0     0
Otu206    20     0     0     9     0     0     0     0     0     0     0     0
Otu207     0     0     0     0     0     0     0     0     0     0     0     0
Otu208     0     0     0     0     0     0     0     0     0     0     0     0
Otu209     0     0     0     0     0     0     0     0     0     0     0     0
Otu210     0     0     6     0     0     0     0     0     0     0     0     0
Otu211     0     7     0     0     0     0     0     0    11    30     0     0
Otu212     0     0     0     0     0     0     0     0    79     0     0     0
Otu213    78     0     0     0     0     0     0     0     0     0     0     0
Otu214     0     0     0     0     0     0     0     0     0     0     0     0
Otu215     0     0     0     0     0     0     0     0     0     0     0     0
Otu216     0     0     0     0     0     0     0     0     0     0     0     0
Otu217     5     5     0    30     0     0     0     0     0     0     0     0
Otu218     2     0     0     0    13     0     0     0     0     0     0     0
Otu219     1     2     0     0     0     0     0     1     6    11     2     0
Otu220    63     0     0     0     0     0     0     0     0     0     0     0
Otu221     0     0     0     0     0     0     0     0     0     0     0     0
Otu222     0     0     3     0     0     0     0     0     0     0     0     0
Otu223     0    47     0     0     0     0     0     0     0     0     0     0
Otu224    59     0     0     0     0     0     0     0     0     0     0     0
Otu225     0     0     0     0     0     0     0     0     0     0     0     0
Otu226     0     0     0     0     0     0     0     0     0     0     0     0
Otu227     0     1     1     0     0     0     0     0     7     9     0     0
Otu228     0     0     5     0     0     0     0     0     0     0     0     0
Otu229     0     0     0     0     0     0     0     0     0     0     0     0
Otu230     0     0     4     0     0     0     0     0     0     0     0     0
Otu231    43     0     0     0     0     0     0     0     0     0     0     0
Otu232     0     0     0     0     0     0     0     0     0     0     0     0
Otu233     0     0     0     0     0     0     0     0     0     0     0     0
Otu234     0     0     3     0     0     0     0     0     0    12     2     0
Otu235     0     0     0     0     0     0     0     0     8    16     0     0
Otu236     0     0     0     0     0     0     0     0     0     0     0     0
Otu237     0     0     0     0     0     0     0     0     0     0     0     0
Otu238     0     0     0     0     3     0     8     0     0     0     0     0
Otu239     0     0     0     0     0     0     0     0     0     0     0     0
Otu240     0     0     0     0     0     0     0     0     0     0     0     0
Otu241     0     0     0     0     0     0     0     0     0     0     0     0
Otu242     2     0     4     0     0     0     0     0     2     6     0     0
Otu243     1     0     0     0     0     0     0     0     0     0     0     0
Otu244     0     0     0     0     0     0     0     0     0     0     0     0
Otu245     0     0     0     0     0     0     0     0     0     0     0     0
Otu246     0     0     0     0     0     0     0     0     0     0     0     0
Otu247     0     0     0     0     0     0     0     0     0     0     0     0
Otu248     0     0     0     0     0     0     0     0     0     0     0     0
Otu249     0     0     0     0     0     0     0     0     0     0     0     0
Otu250     0     7     0     0     0     0     0     0     0     0    17     0
Otu251     0     0     2     0     0     0     0     0     0     0     0     0
Otu252     0     0     0     0     0     0     0     0     0     0     0     0
Otu253     0     0     0     0     0     0     0     0     0     0     0     0
Otu254     0     0     1     0     0     0     0     0     0     2     1     0
Otu255     0     0     0     0     0     0     0     0     0     0     0     0
Otu256     0     0     0     0     0     0     0     0     0     0     0     0
Otu257     1     0     0     0     0     0     0     0     0     0     0     0
Otu258     0     0     0     0     0     0     0     0     0     0     0     0
Otu259     0     0     0     0     0     0     0     0     0     0     1     0
Otu260     0     0     0     0     0     0     0     0     0     0     0     0
Otu261     0     0     0     0     0     0     0     0     0     0     0     0
Otu262     0    19     0     0     0     0     0     0     0     0     0     0
Otu263     0     0     0     0     0     0     0     0     0     0     0     0
Otu264     0     0     0     0     0     0     0     0     0     0     0     0
Otu265     0     0     0     0     0     0     0     0     0     0     0     0
Otu266     2     0     0     0     0     0     0     0     0     0     0     0
Otu267     0     0     0     0     0     0     0     0     0     0    16     0
Otu268     0     0     1     0     0     0     0     0     1     0     0     0
Otu269     0     0     0     0     0     0     0     0     0     0     0     0
Otu270     0     0     0     0     0     0     0     0     0     0     0     0
Otu271     0     0     0     0     0     0     0     0     0     0    15     0
Otu272     0     0     0     0     0     0     0     0     0     0     0     8
Otu273     0     0     0     0     0     0     0     0     0     0     0    10
Otu274     0     0     0     9     0     0     0     0     0     0     0     0
Otu275     0     0     0     0     0     0     0     0     0     0     0     0
Otu276     0     0     0     0     0     0     0     0     0     0     0     0
Otu277     0     0     0     0     0     0     0     0     0     0     0     0
Otu278     0    12     0     0     0     0     0     0     0     0     0     0
Otu279     0     0     0     0     9     0     0     0     0     0     0     0
Otu280     0     0     0     0     0     0     0     0     0     0     0     0
Otu281     0     0     0     0     0     0     0     0     0     0     0     0
Otu282     2     0     0     0     0     0     0     0     0     0     0     0
Otu283     0     0     0     0     0     0     0     0     1     4     0     0
Otu284     0     0     0     0     0     0     0     0    11     0     0     0
Otu285     0     0     0     0     0     0     0     0     0     0     0     0
Otu286     0     0     0     0     0     0     0     0     0     0     0     0
Otu287     0     0     0     0     0     0     0     0     0     0     0     0
       X155p X156n X156p X157n X157p X15n  X15p X165n X165p X166n X166p X167n
Otu001     8    25     4     0  7110    6   869  3064     2    16     0    15
Otu002 29899  5387 13459    12  3900 6794    41  4766    50 27259 12317    54
Otu003    25 18206  2287    11 25535    9  9710 27149    15 13570    15    19
Otu004    21     2    14     9     4    9    15     8     5     4     7     0
Otu005     0    14     0     0     0    1     0     0     4     0    13    12
Otu006     0     1     0     6     0    0     0     0    13     0     0     5
Otu007    38     6     0   239    14    0  4437     7  4177  2803  1562     7
Otu008    25     0     0     0     1    0  5682     0     6     3    11     0
Otu009     0     6  2591     0   472  279    10   266     0  1152  1063 15678
Otu010     6     0     0     0     3    1   798     0  6764     9     5     6
Otu011     0     0     8     0    10    3 48298     0     1     0     0     0
Otu012     7 22847     4     0     6    0     0     9    10     8 37498     8
Otu013     0     1    15     1     8    0     7     2     0     0     0     2
Otu014     4     2     2     0     6    1     6     0  2922  2999     7     9
Otu015    19     0     0     0     1 6439     6     0     4     0     0     0
Otu016     9  3220     0     0     1 1944     4     0     1     0  3735     8
Otu017    11    13    15     0     0    0     0     0     0     0     0    14
Otu018  9839     1   977     0     1    1     4     4     0     6     9     1
Otu019     2     0     0     0     0    0     0     0     0     5     0     0
Otu020     0   973     0     0  1631    0  3106   292     0     5   599     0
Otu021     0     0     0     2     0    9     0     0    12     0     0     0
Otu022     6     0  1531     0  1178    0     0   449     1     2  1114 12703
Otu023     1  1053  3960   230     7    0     4     5 10007     4     2     3
Otu024     0     0     0     0    12    0    24     0     0     0     0     0
Otu025     1     0     0     0  1397    0     6  1757     0     0     0     0
Otu026     0     0     0     0     0    0     1     0     6     0     0     5
Otu027     0     0     0     0     8    0    24     3     0     0     0     0
Otu028     0     2  1449   422     1    0     9    12  3568    19     4  2832
Otu029     5     1     2     2     0    2     0  1547     0     0     2     0
Otu030     0     1     3  2910     0    0     0     5 15001     4    10     0
Otu031     5     0     0     0     0    0     0     0     3     0     6     0
Otu032     0     9     0     0  2261    0     0     0     7    15     2     0
Otu033     0     0     0     0     0    0     0     0     1     0     0     5
Otu034     0    12    13 20157    10    4     0    14    11    12    14     0
Otu035     0     2   902     1     0    2     0     1     0     3     0     0
Otu036     0     0     0     0     0    0     0     7     0     0     0     0
Otu037     6     0     0     0     0    0     0     0     0     0     2     0
Otu038     0     1     0     1     0    0     1     0     1     0     0     0
Otu039     0     0     1     1  1195    0    47     0     5     0   354     7
Otu040 10590     0     0     0     0    0     0     1     0     0     3     0
Otu041     2     0   848   554     0    0     0     0  2793     3     3     4
Otu042     0     0     2     1  3327    0     1 10598     0     0     0     0
Otu043     0     0     0     0     0    0     1     2     0     0     0     0
Otu044     2     0     0     0     2    0     2     0     0     2     0     0
Otu045     0     0 10915     0     3    0     0     4     0     2     3     0
Otu046     0     0     0     0     0    2     0     0     1     0     0     0
Otu047     0     2  2106   218     0 2147     0     0     0     0     2     0
Otu048     1     0     0     0     0    0     0     5     0     0     0     0
Otu049     6     0     0     0     4    0     0     0     0     0     0     0
Otu050     0     0     0     0     0    0     0     4     0     0   451     1
Otu051     6     0     9     0     0  149     3     0     0     0    95     0
Otu052     0     0     0     0     0    0     0     0     0     0     0     4
Otu053     1     0     0     0     0    0     0     0     0     0     0     0
Otu054     0     0     1     0     0    0     0     0     0     0     0     2
Otu055     0     0     0     0     0    0     0     0     2     0     0     2
Otu056     0     0     0     0     0    0     0     0     2     0     0     0
Otu057     0     0     1     0     0    0     0     0     0     0     0     0
Otu058     0     0     0     0     1 2352     0     0     0     0     0     0
Otu059     3     0     0     2     0    0     0     0     0     0     4     0
Otu060     0     0     0     0     0    0     0     0     0     0     0     0
Otu061     0     0     0     0     0    0     0     0     0     0     0     0
Otu062     0     0     0     0     0    0     0     0     0     0     0     0
Otu063     0     3     0     0     0    0     0     0     0     0     0     6
Otu064     0     0     0     0     0    0     0     0     0     0     0     0
Otu065     0     0     0     0     2    0  4528     0     0     0     0     0
Otu066     1     0     0     0   783    0     1     6     0   180     0     0
Otu067     0     2     0  1796     0   26     0     0     1     0   291     2
Otu068     0     0     0     0     0    0     1     0     0     0     0     0
Otu069     0     0     0     0     0  347     0     0     0     0     0     4
Otu070     1     0     0   307     0    0     2     0     0     0     0     0
Otu071     0     0     0     0     0    0     0     0     1     0     0     0
Otu072   218     0    46    78     0   11     0     0     0    11     0     0
Otu073     0     0     0     0     0    0     0   242     0     0     0     0
Otu074     0     0     0     0     0    0     0    30     0     3     0     1
Otu075     4     0     0   170     1    0     0     0     0     0     3     0
Otu076     0     0     0     0     0    0     0     0     0     0     0     0
Otu077     0     0     0     0     0    0     0     0     0     0     0     0
Otu078     0     0     0     0     0  188     0     0    40     0     1     0
Otu079     0     3     0     0     0    0     0     0     0     0     0     3
Otu080     0     0     0     0     0    0     0     0     0     0     0     0
Otu081     0     0     0     0     0    0     0     0     2     0     0     0
Otu082     0     0     0     0     0    0     0     0     0     3     0     0
Otu083     1     0     0     0     0    0     0     0     0     0     1     0
Otu084     0     0     0     0     0    0     0     0     0     0     0     0
Otu085     0     0  1903     0     0    0     0     0     0     0     1     0
Otu086     0     0     0     0     0    0     0     0     0     1     0     0
Otu087     0     0     0     0     0    0     0     0     1     0     0     0
Otu088     0     0     0     0     0    0     0     0     2     0     0     0
Otu089     0     0     0     0     0    0     0     0     0     0     0     0
Otu090     0     0     0     0     0    0     0     0  3033     0     3     0
Otu091     0     0     0     0     0    2     0     0     0     0     0     0
Otu092     0     0     0     0     0    0     0     0     0     0     0     1
Otu093     0     0     0     0     0    0     0     0     0     0     0     0
Otu094     0     0     0     0     0    0     0     0     0     0     0     0
Otu095     0     0     0     1     0    0     0     0     0     0  1761     0
Otu096     0     0     0     0     0    0     0     0     0     0     0     0
Otu097     0  2323     0     0     0    0     0     0     0     0     0     0
Otu098     0     2     0     0     0    0     0     0     1  2345     0     0
Otu099     0     0     0     0     0    0     0     0     0     0     0     0
Otu100     0     0     0     0     0    0     0     0     0     0     0     0
Otu101     0     0     0     0     0    0     0     0     0     0     0     0
Otu102     0     0     0   276     0    0     0     0     0     0     0     0
Otu103     0     0     0     0     0   46     0     1     0     0     0     0
Otu104     0     0     0     0     0    0     0     0     0     0     0     0
Otu105     0     0     0     0     0    0     0     0     0     0     0     0
Otu106     1     0     0     0     0    0     0     0     0     0     0     0
Otu107     0     0     0     0     0    0     0     0     0  1846     0     0
Otu108     0     0     0     0     0    0     0     1     0     0     0     0
Otu109     0     0     0     0     0    1     0     0     0     0     0     0
Otu110     0     2     0     0   487    0     0     0     0   871   390     0
Otu111     0     0     0     0     0 1467     0     0     0     0     0     0
Otu112     0     1     0     0     0    0     0     0     0     0     0     0
Otu113     0     0     0     0     0    0     0   291     0     0   235     0
Otu114     0     0     0     0    26    0    10    11     0     0     0     0
Otu115     0     0     0     0     0    0     0     0     0     0     0     0
Otu116     0     0     0  1518     3    1     0     0     1     1     1     0
Otu117     0     0     0     0     0    0     0     0     0     0     0     0
Otu118     0     0     0     0     0    0     0     0     0     0     0     0
Otu119     0     1     0     4     0    6     0     1     0     0     0     0
Otu120     1    50     2     0    72    0    12    73     0    22     0     0
Otu121     0     0     0     0     0    0     0     0     0     0     1     0
Otu122     0     0     0     0     0    0     0     0     0     0     0     0
Otu123     0     0     0     0    10    0     1     8     0     0     0     0
Otu124     0     0     0     0     0    0     0     0     0     0     0     0
Otu125     0     0   784     0     0  106     0     0     0     0     0     0
Otu126     0     0     0     0     0    0     0     0     0     1   931     0
Otu127     0     0     0     0     1    0     0     0     0     0     0     0
Otu128     0    61     0     0     0   61     0     0     0     0    72     0
Otu129     0     0     0     0   913    0     0     0     0     1     0     0
Otu130     0     0     0     0     0    0     0     0     0     0     0     0
Otu131     1     0     0     0     0    0     0     0     0     0     0     0
Otu132     0     0     0     0     0    0     0     0     0     0     0     0
Otu133     0     0     0     0     0    0     0     0     0     0     0     0
Otu134     0     0     0     0     0    0     0     0     0     0     0     0
Otu135     0     0     0     0     0    0     0     0     0     0     0     0
Otu136     0     0     0     0     0    0     0     0     0     0     0     0
Otu137     0     0     0     0   722    0     0     0     0     0     0     0
Otu138     0     0     0     0     0    0   218     0     0     0     0     1
Otu139     0   694     0     0     0    0     0     0     0     0     0     0
Otu140     0     0     0     0     0    0     0     0     0     0     0     0
Otu141     0     0     0     0    57    0     2     0     0     1     0     0
Otu142     0     0     0     0     0    0     0     0     0     0     0     0
Otu143     0     0     0     0     0    0     0     0     0     0     0     0
Otu144     0     0     0     0     0    0     0     0     0     0     0     0
Otu145     0     0     0     0     0    0     0     0     0     0     0     0
Otu146     0     0     0     0     0    0     0     0     0     0     0     0
Otu147     0     0     0     0     0    0     0     0     0     0     0     0
Otu148     0     0     0     0     0    0     0     0     0     0     0     0
Otu149     0     0     1     0   559    0     0     0     1     0     0     0
Otu150     0     0     0     0     0    0     0     0     0     0     0     0
Otu151     0     0     0     0     0    0     0     0     0     0     0     0
Otu152     0     0     0     0     0    0     0     0     0     0     0     0
Otu153     0     0     0     0     0    0     0     0     0     0     0     0
Otu154     0     0     0     0     0    0     0     0     0     0     0     0
Otu155     0     0     0     0     0    0     0     0     0     0     0     0
Otu156     0    31     2     0    32    0     4    31     0    25     0     0
Otu157     0     0     0     0     0    0     0     0     0     0     0     0
Otu158     0     0     0     0     0    0     0     0     0     0     0     0
Otu159     0     0     0     0     0    0     0     0     0     0     0     0
Otu160     0     0     0     0     0    0     0     0     0     0     0     0
Otu161     0    27     0     0     0   16     0     0     0     0    32     0
Otu162     0     0     0     0     0    0     0     0     0     0     0     0
Otu163     0     0     0     0     0    0     0     0     0     1     0     0
Otu164     0     0     0     0     0    0     0     0     0     0     0     0
Otu165     0     0     0     0     0    0     0     0     0     0     0     0
Otu166     0     0     0     0     0    0     0     0     0     0     0     0
Otu167     0     0     0     0     0    0     0     0     0     0     0     0
Otu168     0     0     0     0     0    0     0     0     0     0     0     0
Otu169     0     0     0     0     0   16     0     0     0     0    12     0
Otu170     0     0     0     0     0    0     0     0     0     0     0     0
Otu171     0     0     0     0     0    0     0     0     0     0     0     0
Otu172     0     0     0     0     0    0     0     0     0     0     0     0
Otu173     0     0     0     0     0    0     0     0     0     0     0     0
Otu174     0     0     0     0     0    0     0     0    11     1     0     0
Otu175     0     0     0     0     0    0     0     0     0     0     0     0
Otu176     0     0     0     0     0    0     0     0     0     0     0     0
Otu177     0     0     0     0     0    0     0     0     0     0     0     0
Otu178     0     0     0     0     0    0     0     0     0     0     0     0
Otu179     0     0     0     0     0    0     0     0     0     0     0     0
Otu180     0     0     0     0     0    0     0     0     0     0   193     0
Otu181     0     0     0     0     0    0   132     0     0     0     0     0
Otu182     0     2     3     0     4    0    19     8     0     6     0     0
Otu183     0     0     0     0     0    0   123     0     0     0     0     0
Otu184     0     0     0     0     0    0     0     0     0   156     0     0
Otu185     0     3     1     0    14    0     3    14     0    10     0     0
Otu186     0     0     0   148     0    0     0     0     0     0     0     0
Otu187     0     9     0     0     0    8     0     0     0     0    14     0
Otu188     0    10     1     0    17    0     7    14     0     0     0     0
Otu189     0     0     0     0     0    0   103     0     0     0     0     0
Otu190     0     0     0     0     0    0     0     0     0     0     0     0
Otu191     0     0     0     0     0    0     0     0     0     0     0     0
Otu192     0     0     0     0     0    0     0     0     0     0     0     0
Otu193     0     0     0     0     0    0     0     0     0     0     0     0
Otu194     0     0     0     0     0    0     0     0     0     0     0     0
Otu195     0     0     0     0     0    0     0     0     0     0     0     0
Otu196     0     0     0     0     0    0     0     0     0     0     0     0
Otu197     0     0     0     0     0    0     0     0     0     0     0     0
Otu198     0     0     0     0     0    0     0     0     0     0     0     0
Otu199     0     0     0     0     0    0     0     0     0     0     0     0
Otu200     0     0     0     0     0    0    93     0     0     0     0     0
Otu201     0     0     0     0     0    0     0     0     0     0     0     0
Otu202     0     0     0     0     0    0     0     0     0     0     0     0
Otu203     0     0     0     0     0    0     0     0     0     0     0     0
Otu204     0     0     0     0     0    0     0     0     0     0     0     0
Otu205     0     0     0     0     0    0     0     0     0     0     0     0
Otu206     0     0     3     0     0    0     0     0     0     0     0     0
Otu207     0     0     0     0     0    0     0     0     0     0     0     0
Otu208     0     0     0     0     0    0     0     0     0     0     0     0
Otu209     0     0     0     0     0    0     0     0     0     0     0     0
Otu210     0     0     0     0     0    0     0     1     0     0     0     0
Otu211     0     0     0     0     5    0     0     2     0     0     0     0
Otu212     0     0     0     0     0    0     0     0     0     0     0     0
Otu213     0     0     0     0     0    0     0     0     0     0     0     0
Otu214     0     0     0     0     0    0     0     0     0     0     0     0
Otu215     0     0     0     0     0    0     0     0     0     0     0     0
Otu216     0    34     0     0     0    0     0     0     0     0    37     0
Otu217     0     0     0     0     0    0     0     0     0     0     0     0
Otu218     0     0     0     0     0    0     0     0     0     0     0     0
Otu219     0     1     0     0     6    0     0     3     0     5     0     0
Otu220     0     0     0     0     0    0     0     0     0     0     0     0
Otu221     0     0     0     0     0    0     0     0     0     0     0     0
Otu222     0     0     0     0     0    0     0     1     0     0     0     0
Otu223     0     0     0     0     0    0     0     0     0     0     0     0
Otu224     0     0     0     0     0    0     0     0     0     0     0     0
Otu225     0     0     0     0     0    0     0     0     0     0     0     0
Otu226     0     0     0     0     0    0     0     0     0     0     0     0
Otu227     0     2     1     0     6    0     1     4     0     1     0     0
Otu228     0     0     0     0     0    0     0     0     0     0     0     0
Otu229     0     0     0     0     0    0     0     0     0     0     0     0
Otu230     0     0     0     0     1    0     0     1     0     0     0     0
Otu231     0     0     0     0     0    0     0     0     0     0     0     0
Otu232     0     0     0     0     0    0     0     0     0     0     0     0
Otu233     0     0     0     0     0    0     0     0     0     0     0     0
Otu234     0     4     0     0     0    0     0     3     0     3     0     0
Otu235     0     0     0     0     0    0     0     1     0     0     0     0
Otu236     6     0     0     0     1    0     0     0     0     0     0     0
Otu237     0     0     0     0     0    0     0     1     0     0     0     0
Otu238     0     0     3     0     0    0     0     0     0     0     0     0
Otu239     0     0     0     0     0    0     0     0     0     0     0     0
Otu240     0     0     0     0     0    0     0     0     0     0     0     0
Otu241     0     0     0     0     0    1     0     0     0     0     0     0
Otu242     0     2     1     0     2    0     1     2     0     0     0     0
Otu243     0     0     0     0     0    4     0     0     0     0     1     0
Otu244     0     0    28     0     0    0     0     0     0     0     0     0
Otu245     0     0     0     0     0    0     0     0     0     0     0     0
Otu246     0     0     0     0     0    0     0     0     0     0     0     0
Otu247     0     0     0     0     0    0     0     0     0     0     0     0
Otu248     0     0     0     0     0    0     0     0     0     0     0     0
Otu249     0     0    12     0     0    0     0     0     0     0     0     0
Otu250     0     0     0     0     0    0     0     0     0     0     0     0
Otu251     0     0     0     0     0    0     0     0     0     0     0     0
Otu252     0     0     0     0     0    0     0     0     0     0     0     0
Otu253     0     0     0     0     0    0     0     0     0     0     0     0
Otu254     0     1     0     0     7    0     1     0     0     0     0     0
Otu255     0     0     0     0     0    0     0     0     0     0     0     0
Otu256     0     0     0     0     0    0     0     0     0     0     0     0
Otu257     0     0     7     0     0    3     0     0     0     0     0     0
Otu258     0     1     0     0     0    3     0     0     0     0     2     0
Otu259     0     0     0     0     0    0     0     0    18     0     0     0
Otu260     0     0     0     0     0    0     0     0     0     0     0     0
Otu261     0     0     0     0     0    0     0     0     0     0     1     0
Otu262     0     0     0     0     0    0     0     0     0     0     0     0
Otu263     0     0     0     0     0    0     0     0     0     0     0     0
Otu264     0     4     0     0     0    0     0     0     0     0     0     0
Otu265     0     0     0     0     0    0     0     0     0     0     0     0
Otu266     0     1     0     0     0    0     0     0     0     0     2     0
Otu267     0     0     0     0     0    0     0     0     0     0     0     0
Otu268     0     3     0     0     5    0     0     1     0     0     0     0
Otu269     0     0     0     0     0    0     0     0     0     0     0     0
Otu270     0     1     0     0     0    1     0     0     0     0     0     0
Otu271     0     0     0     0     0    0     0     0     0     0     0     0
Otu272     0     0     0     0     0    0     0     0     0     0     0     0
Otu273     0     0     0     0     0    0     0     0     0     0     0     0
Otu274     0     0     0     0     0    0     0     0     0     0     0     0
Otu275     0     0     0     0     0    0     0     0     0     0     0     0
Otu276     0     0     0     0     0    0     0     0     0    12     0     0
Otu277     0     0     0     0     0    0     0     0     0     0     0     0
Otu278     0     0     0     0     0    0     0     0     0     0     0     0
Otu279     0     0     0     0     0    0     0     0     0     0     0     0
Otu280     0     0     0     0     0    0     0     0     0     0     0     0
Otu281     0     0     0     0     0    0    12     0     0     0     0     0
Otu282     0     0     0     0     0    0     0     0     0     0     0     0
Otu283     0     0     0     0     3    0     0     0     0     1     0     0
Otu284     0     0     0     0     0    0     0     0     0     0     0     0
Otu285     0     0     0     0     0    0     0     0     0     0     0     0
Otu286     0     0     0     0     0    0     0     0     0     0     0     0
Otu287     0     0     0     1     0    0     0     0     7     0     0     0
       X167p   X1n  X1p  X2n   X2p   X3n   X3p  X5n   X5p   X7n   X7p  X9n  X9p
Otu001     6 34898   38  961 66205 90380    32 2225    32 12541   651 6453 9453
Otu002    12  1308 2348   14  3222  3481    27   37    48 10010    16 1666   23
Otu003  1519  4804   17    9 10849  9941    24 5173    10    23     8 4933 8939
Otu004    13  2585   40    7  6698  4494    10   35 20980     8 14922    6   12
Otu005     0 14196    7 6756     6     6 18437    4 23695    15     0    2    0
Otu006     0 13588 5905 8730     1    12 50272    5   778     0     0    0    0
Otu007     0  4219    0  431  4161     3  1988    9    25     9     3    1 7972
Otu008     1     0    1    0     0     0   127    5 14577   762     2    0  752
Otu009     0     9 7552   11     0     5     2    3     1  1520   675   64    3
Otu010     4     0    0    0     4     1     3    8     8     0     0    1 5860
Otu011     5     0    8    0    15     0     0    0     0     0     0    1 7696
Otu012     0    15    0    0     0     0     0    0    22     8     0    0    0
Otu013    15  4960   22    0 13823     8  3576    0     0     2    12  893    4
Otu014 16669     4    7    0     4     0     0    4     8  2637     0    1    5
Otu015     0     0    0    5     4     0    20    0     0     3     0 1155    5
Otu016     5     2    0    0     0     2     0    0    12     1     0  325    0
Otu017    12    16   27    0     0     0     0    0     0    10    15    0    0
Otu018     5     0   13    1     0     0     0   18     4  2104     7    1    0
Otu019     0     0    0    0     0     0     0   16     0     0     0    0    0
Otu020     1     0 2028    0     0     1     1  957     0     1  1267    0  431
Otu021     0     5    4 6695     0     9 23193    6    12     0     0    3    0
Otu022     0     5    3   11     3     0    31    0     2     6     4    0    0
Otu023  1582     1    0    0     3     3     7    0     0  2053     0    0    0
Otu024     0     0    0    0    15     0     0    0     0     0     0    0    8
Otu025     0   174    0    0     6    15     0    0   583     0     0    0    0
Otu026  5612     0    2    0     5     0     8    0     0     0     2    0    0
Otu027     0     0    0    0    15    12     2    0     0     0     1    0    7
Otu028     0   549    3  290     0     9  3633    1  1464    91     1    0 2242
Otu029  5554     1    1    4     0     2     0    0     0     1    12    0    0
Otu030     0     5    1 2755     2     1  2418    1     2     0     0    0    0
Otu031     0     5    1    1     1     0     5    1 10578     1  1223    0    0
Otu032     0     0    0    0     5     0    21   22     0     0     0    0    0
Otu033     0     0    0    0     0     0     5    0     0     0     0    0    0
Otu034     0     0    0   11     0     0     0    0     0     0     0    0    0
Otu035     5     3    1    5     0     0     0 7464     0   710     0    0    1
Otu036     0     0    2    0     0 18980     3    0     0     0     0    0    0
Otu037     0     2    0 1111     4     4    35    2 17372     0     0    0    0
Otu038     1     7    0    1     0     0     2    0     2  3637     0    0    0
Otu039     0     0    0    0     0     0     6    0     0     3   883    0    4
Otu040     0     0    0    0     0     0     0    0    11     3   415    0    0
Otu041     0     0    2    3     0     0     3    2  2596   336     1    0    0
Otu042     0     0    0    0     1     9     0    0     0     0     0    0    3
Otu043     0     0    0    0     0     4     0    0     0     1     0    0    0
Otu044     0     0    0    0     0     0     0    0     0     1     1  430    0
Otu045     3     0    5    0     0     0     0    0     0     0     0    0    0
Otu046     0     1    2 8776     4     4  1709    1     3     0     0    0    0
Otu047     0     2    3    0     0     1     0    0     4   641     0  338    0
Otu048     0     0    0    0     0     9     0    0     0     0     0    0    0
Otu049     0     0    0    0     4     0     0    0     3     0     0    0    5
Otu050  3614     0    0    0     0     4     0    0     0     0     0    0    1
Otu051     0   548    0    0     0     0     0    0   238     0     4   21    0
Otu052     0     0    0    0     0     2     0    0     0     0     0    0    0
Otu053     0     0    0    0     0     9     0    0     0     0     1    0    0
Otu054  8853     0    5    0     0     0     0    0     0     0     3    0    0
Otu055     0     0    0    0     0     0     0    0     0     0     0    0    0
Otu056     0     0    0    0     0     0     2    0     0     0     0 1742    0
Otu057     0     0    0    0     0     0     0    3     0     0     0    0    0
Otu058     0     0    0    0     4     0     0    0     0     0     0  556    0
Otu059     0   608    2 1141     2     0  1671    1  4358     0     0    0    0
Otu060     0     0    0    0     0     0     2    0     0     0     0    0    0
Otu061     0  6627    0    0     0     1     0    0     0     4     0    0    0
Otu062     0   789    0    0     2     0  4016    0  1772     0     0    0    0
Otu063     0     6    0    0     0     0     0    0     0     0     0    0    0
Otu064  6177     0    2    0     0     0     0    0     0     0     0    0    0
Otu065     0     0    0    0     1     0     0    0     0     0     0    0  669
Otu066     0     9    0    0     0     0     0    0     0    48     0    0    2
Otu067     0     1    0  360     0     0   927    0     1     1     0   14    0
Otu068     3     0    4    0     0     0     0    0     0     0  1098    1    0
Otu069     0     0    0    0     0     0     0    0     0  1891     0   83    0
Otu070     0     1    0  274     2     0     0    0   996     0     0    0    2
Otu071     0     0    0    0     0     0  4881    0     0     0     0    0    0
Otu072     0     0  104   42     0     0     0    0     0    31    36    4    0
Otu073     0     0    0    0     0     1     1    0     0     0     0    0    0
Otu074    10  1304 1024  209     1    12  1660    0     1     0    28    0    0
Otu075     0     0    0    0     0     4     0    0     2     0     0    0    0
Otu076     0     0    0    0     0     3     0    0     0     0     0    0    0
Otu077     0     0    0    0     0     0     0    0     0     0     0    0    0
Otu078     0     0    0    0     0     0   840    0    96   213     0   26    0
Otu079     0     5    0    0     0     0     0    0     0     3     0    0    0
Otu080     0     0    1    0     0     0     0    0     0     1   859    1    0
Otu081     0     0    2    0     1     0  3865    0     0     0     0    0    0
Otu082     0   519    0    0  1665     0     0 1653     0     0     0    0    0
Otu083     0     0    0    0     0     0     0    0  3820     0     0    0    0
Otu084     0     0    0    0     0     0     3    0     0     0     0    0    0
Otu085     0     0    2    0     0     0     0    0     0     0     0    0    0
Otu086     0     2    0    0     0     0     0 3386     0     0     0    0    0
Otu087     0     6    0 1575     1     0  1691    0     1     0     0    0    0
Otu088     0     0    0    0     0     0     0    0     0     0     0    0    0
Otu089     0     0    1    0     0     1  3059    0     3     0     0   46    0
Otu090     0     0    0    0     0     0     6    0     0     0     0    0    0
Otu091     0     1    0 1630     0     0  1288    1     2     0     0    0    0
Otu092     0     0    0    0     0     0     0    1     0     0     0    0    0
Otu093     0  1131    0    0     0     0     0    0  1475     2     0    0    0
Otu094     0     0    0    0     0     0     0    0     0     0     0    0    0
Otu095     0     0    0    0     0     0     0    2     1     0     0    0    0
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Otu097     0     1    0    0     0     0     0    0     0     0     0    0    0
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       tri01n tri01p tri02n tri02p tri03n tri03p
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Otu009      2  14476      5      0      0    695
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Otu127      0      0      0      0      0      0
Otu128      0      0      0      0      0    658
Otu129      0      0      0      0      0      0
Otu130      0      0      0      0      0      0
Otu131      0      0      0      0      0      0
Otu132      0      0      0      0      0      0
Otu133      0      1      0      0      0      0
Otu134      0      0      0      0      0      0
Otu135      0      0      0      0      0      0
Otu136      0      0      0      0      0      0
Otu137      0      0      0      0      0      0
Otu138      0      0      0      0      0      0
Otu139      0      0      0      0      0      0
Otu140      0      0      0      0      0      0
Otu141      0      0      0      0      0      0
Otu142      0      0      0      0      0      0
Otu143      0      0      0      0      0      1
Otu144      0      0      0      0      0      0
Otu145      0      0      0      0      0      0
Otu146      0      0      0      0      0      0
Otu147      0      0      0      0      0      0
Otu148      0      0      0      0      0      0
Otu149      0      1      0      0      0      0
Otu150      0      0      0      0      0      0
Otu151      0      0      0      0      0      0
Otu152      0      0      0      0      2      0
Otu153      0      0      0      0      0      0
Otu154      0      0      0      0      0      0
Otu155      0      0      0      0      0      0
Otu156      0      0      0      0      0      0
Otu157      0      0      0      0      0      0
Otu158      0      0      0      0      0      0
Otu159      0      0      0      0      0      0
Otu160      0      0      0      0      0      0
Otu161      0      0      0      0      0    258
Otu162      0      0      0      0      0      0
Otu163      0      0      0      0      0      0
Otu164      0      0      0      0      0      0
Otu165      0      0      0      0      0      0
Otu166      0      0      0      0      0      0
Otu167      0      0      0      0      0      0
Otu168      0      0      0      0      0      0
Otu169      0      0      0      0      0    229
Otu170      0      0      0      0      0      0
Otu171      0      0      0      0      0      0
Otu172      0      0      0      1      0      0
Otu173      0      0      0      0      0      0
Otu174      0      0      0      0      0      0
Otu175      0      0      0      0      0      0
Otu176      0      0      0      0      0      0
Otu177      0      0      0      0      0      0
Otu178      0      0      0      0      0      0
Otu179      0      0      0      0      0      0
Otu180      0      0      0      0      0      0
Otu181      0      0      0      0      0      0
Otu182      0      0      0      0      0      0
Otu183      0      0      0      0      0      0
Otu184      0      0      0      0      0      0
Otu185      0      0      0      0      0      0
Otu186      0      0      0      0      0      0
Otu187      0      0      0      0      0    107
Otu188      0      0      0      0      0      0
Otu189      0      0      0      0      0      0
Otu190      0      0      0      0      0      0
Otu191      0      0      0      0      0      0
Otu192      0      0      0      0      0      0
Otu193      0      0      0      0      0      0
Otu194      0      0      0      0      0      0
Otu195      0      0    124      0      0      0
Otu196      0      0      0      0      0      0
Otu197      0      0      0      0      0      0
Otu198      0      0      0      0      0      0
Otu199      0      0      0      0      0      0
Otu200      0      1      0      0      0      0
Otu201      0      0      0      0      0      0
Otu202      0      0      0      0      0      0
Otu203     95      1      0      0      1      0
Otu204      0      0      0      0      0      0
Otu205      0      0      0      0      0      0
Otu206     19      0      0      0      0      0
Otu207      0      0      0      0      0      0
Otu208      0      0      0      1      0      0
Otu209      0      0      0      0      0      0
Otu210      0      0      0      0      0      0
Otu211      0      0      0      0     22      0
Otu212      0      0      0      0      0      0
Otu213      0      0      0      0      0      0
Otu214      0      0      0      0      0      0
Otu215      0      0      0      0      0      0
Otu216      0      0      0      0      0      0
Otu217     15      0      1      0      0      0
Otu218      0      0      0      0      0      0
Otu219      0      0      0      0      0      0
Otu220      0      0      0      0      0      0
Otu221      0      0      0      0      0      0
Otu222      0      0      0      0      0      0
Otu223      0      0      0      0      0      0
Otu224      0      0      0      0      0      0
Otu225      0      0      0      0      0      0
Otu226      0      0      0      0      0      0
Otu227      0      0      0      0      0      0
Otu228      0      0      0      0      0      0
Otu229      0      0      0      0      0      0
Otu230      0      0      0      0      0      0
Otu231      0      0      0      0      0      0
Otu232      0      0      0      0      0      0
Otu233      0      0      0      0      0      0
Otu234      0      0      0      0      0      0
Otu235      0      0      0      0     12      0
Otu236      0      0      0      0      0      8
Otu237      0      0      0      0      0      0
Otu238      0      0      0      0      0      0
Otu239      0      0      0      0      0      0
Otu240      0      0      0      0      0      0
Otu241      0      0      0      0      0      0
Otu242      0      0      0      0      0      0
Otu243      0      0      0      0      0     22
Otu244      0      0      0      0      0      0
Otu245      0      0      0      0      0      0
Otu246      0      0      0      0      0      0
Otu247      0      0      0      0      0      0
Otu248      0      0      0      0      0      0
Otu249      0      0      0      0      0      0
Otu250      0      0      0      0      0      0
Otu251      0      0      0      0      0      0
Otu252      0      0      0      0      0      0
Otu253      0      0      0      0      0      0
Otu254      0      0      0      0      0      0
Otu255      0      0      0      0      0      0
Otu256      0      0      0      0      0      0
Otu257      0      0      0      0      0      0
Otu258      0      0      0      0      0     14
Otu259      0      0      0      0      0      0
Otu260      0      0      0      0      0      0
Otu261      0      0      0      0      0     18
Otu262      0      0      0      0      0      0
Otu263      0      0      0      0      0      0
Otu264      0      0      0      0      0     14
Otu265      0      0      0      0      0      0
Otu266      0      0      0      0      0     12
Otu267      0      0      0      0      0      0
Otu268      0      0      0      0      0      0
Otu269      0      0      0      0      0      0
Otu270      0      0      0      0      0     12
Otu271      0      0      0      0      0      0
Otu272      0      0      0      0      0      0
Otu273      0      0      0      0      0      0
Otu274      0      0      0      0      0      0
Otu275      0      0      0      0      0      0
Otu276      0      0      0      0      0      0
Otu277      0      0      0      0      0      0
Otu278      0      0      0      0      0      0
Otu279      0      0      0      0      0      0
Otu280      0      0      0      0      0      0
Otu281      0      0      0      0      0      0
Otu282      0      0      0      0      0      0
Otu283      0      0      0      0      0      0
Otu284      0      0      0      0      0      0
Otu285      0      0      0      0      0      0
Otu286      0      0      0      0      0      0
Otu287      0      0      0      0      0      0
In [ ]:
# definir los nombres de las filas de la columna tax

tax_mat <- tax_mat %>%
  tibble::column_to_rownames("otu")
print(tax_mat)
          Domain     Supergroup         Division                Class
Otu001 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu002 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu003 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu004 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu005 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu006 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu007 Eukaryota  Stramenopiles       Ochrophyta        Pelagophyceae
Otu008 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu009 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu010 Eukaryota   Opisthokonta          Metazoa             Craniata
Otu011 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu012 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu013 Eukaryota      Alveolata        Dinophyta          Syndiniales
Otu014 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu015 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu016 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu017 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu018 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu019 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu020 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu021 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu022 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu023 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu024 Eukaryota Archaeplastida     Streptophyta  Klebsormidiophyceae
Otu025 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu026 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu027 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu028 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu029 Eukaryota   Opisthokonta            Fungi           Ascomycota
Otu030 Eukaryota       Hacrobia      Cryptophyta        Cryptophyceae
Otu031 Eukaryota      Alveolata        Dinophyta          Syndiniales
Otu032 Eukaryota Archaeplastida      Chlorophyta    Prasino_Clade_VII
Otu033 Eukaryota Archaeplastida      Chlorophyta          Ulvophyceae
Otu034 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu035 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu036 Eukaryota       Hacrobia       Haptophyta      Haptophyta_HAP2
Otu037 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu038 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu039 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu040 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu041 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu042 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu043 Eukaryota       Hacrobia       Haptophyta      Haptophyta_HAP3
Otu044 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu045 Eukaryota  Stramenopiles  Stramenopiles_X             Bicoecea
Otu046 Eukaryota Archaeplastida      Chlorophyta        Chlorophyceae
Otu047 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu048 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu049 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu050 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu051 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu052 Eukaryota Archaeplastida     Streptophyta        Embryophyceae
Otu053 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu054 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu055 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu056 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu057 Eukaryota Archaeplastida     Streptophyta        Embryophyceae
Otu058 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu059 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu060 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu061 Eukaryota      Alveolata        Dinophyta          Syndiniales
Otu062 Eukaryota Archaeplastida      Chlorophyta      Pyramimonadales
Otu063 Eukaryota       Hacrobia       Haptophyta         Haptophyta_X
Otu064 Eukaryota   Opisthokonta            Fungi           Ascomycota
Otu065 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu066 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu067 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu068 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu069 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu070 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu071 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu072 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu073 Eukaryota  Stramenopiles       Ochrophyta        Pelagophyceae
Otu074 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu075 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu076 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu077 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu078 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu079 Eukaryota      Alveolata        Dinophyta          Syndiniales
Otu080 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu081 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu082 Eukaryota   Opisthokonta Choanoflagellida    Choanoflagellatea
Otu083 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu084 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu085 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu086 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu087 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu088 Eukaryota  Stramenopiles       Ochrophyta        Pelagophyceae
Otu089 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu090 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu091 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu092 Eukaryota Archaeplastida      Chlorophyta      Pyramimonadales
Otu093 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu094 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu095 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu096 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu097 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu098 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu099 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu100 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu101 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu102 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu103 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu104 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu105 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu106 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu107 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu108 Eukaryota Archaeplastida      Chlorophyta        Chlorophyceae
Otu109 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu110 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu111 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu112 Eukaryota Archaeplastida     Streptophyta        Embryophyceae
Otu113 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu114 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu115 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu116 Eukaryota      Alveolata        Dinophyta          Syndiniales
Otu117 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu118 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu119 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu120 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu121 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu122 Eukaryota   Opisthokonta          Metazoa           Arthropoda
Otu123 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu124 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu125 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu126 Eukaryota       Hacrobia      Cryptophyta        Cryptophyceae
Otu127 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu128 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu129 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu130 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu131 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu132 Eukaryota      Amoebozoa           Lobosa            Tubulinea
Otu133 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu134 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu135 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu136 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu137 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu138 Eukaryota Archaeplastida     Streptophyta        Embryophyceae
Otu139 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu140 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu141 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu142 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu143 Eukaryota  Stramenopiles  Stramenopiles_X      Stramenopiles_X
Otu144 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu145 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu146 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu147 Eukaryota  Stramenopiles  Stramenopiles_X                 MAST
Otu148 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu149 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu150 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu151 Eukaryota Archaeplastida      Chlorophyta      Prasinococcales
Otu152 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu153 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu154 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu155 Eukaryota       Hacrobia        Telonemia            Telonemia
Otu156 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu157 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu158 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu159 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu160 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu161 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu162 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu163 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu164 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu165 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu166 Eukaryota   Opisthokonta            Fungi           Ascomycota
Otu167 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu168 Eukaryota Archaeplastida      Chlorophyta     Trebouxiophyceae
Otu169 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu170 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu171 Eukaryota Archaeplastida      Chlorophyta      Pyramimonadales
Otu172 Eukaryota      Alveolata        Dinophyta          Syndiniales
Otu173 Eukaryota   Opisthokonta            Fungi           Ascomycota
Otu174 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu175 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu176 Eukaryota Archaeplastida      Chlorophyta        Chlorophyceae
Otu177 Eukaryota Archaeplastida      Chlorophyta        Chlorophyceae
Otu178 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu179 Eukaryota  Stramenopiles       Ochrophyta         Ochrophyta_X
Otu180 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu181 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu182 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu183 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu184 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu185 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu186 Eukaryota Archaeplastida      Chlorophyta     Prasino_Clade_IX
Otu187 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu188 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu189 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu190 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu191 Eukaryota       Rhizaria         Cercozoa Chlorarachniophyceae
Otu192 Eukaryota Archaeplastida     Streptophyta  Klebsormidiophyceae
Otu193 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu194 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu195 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu196 Eukaryota      Alveolata       Ciliophora         Spirotrichea
Otu197 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu198 Eukaryota   Opisthokonta            Fungi      Chytridiomycota
Otu199 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu200 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu201 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu202 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu203 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu204 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu205 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu206 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu207 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu208 Eukaryota Archaeplastida      Chlorophyta        Chlorophyceae
Otu209 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu210 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu211 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu212 Eukaryota Archaeplastida     Streptophyta  Klebsormidiophyceae
Otu213 Eukaryota  Stramenopiles       Ochrophyta        Bolidophyceae
Otu214 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu215 Eukaryota Archaeplastida      Chlorophyta    Prasino_Clade_VII
Otu216 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu217 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu218 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu219 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu220 Eukaryota Archaeplastida      Chlorophyta      Prasinococcales
Otu221 Eukaryota Archaeplastida      Chlorophyta        Chlorophyceae
Otu222 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu223 Eukaryota      Amoebozoa           Lobosa            Tubulinea
Otu224 Eukaryota   Opisthokonta            Fungi        Basidiomycota
Otu225 Eukaryota Archaeplastida      Chlorophyta        Chlorophyceae
Otu226 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu227 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu228 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu229 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu230 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu231 Eukaryota   Opisthokonta            Fungi           Ascomycota
Otu232 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu233 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu234 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu235 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu236 Eukaryota       Hacrobia      Cryptophyta        Cryptophyceae
Otu237 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu238 Eukaryota       Rhizaria         Cercozoa         Sarcomonadea
Otu239 Eukaryota   Opisthokonta          Metazoa           Arthropoda
Otu240 Eukaryota      Alveolata        Dinophyta          Syndiniales
Otu241 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu242 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu243 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu244 Eukaryota  Stramenopiles  Stramenopiles_X      Stramenopiles_X
Otu245 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu246 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu247 Eukaryota  Stramenopiles       Ochrophyta        Pelagophyceae
Otu248 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu249 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu250 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu251 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu252 Eukaryota Archaeplastida      Chlorophyta        Chlorophyceae
Otu253 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu254 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu255 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu256 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu257 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu258 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu259 Eukaryota       Hacrobia      Cryptophyta        Cryptophyceae
Otu260 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu261 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu262 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu263 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu264 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu265 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu266 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu267 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu268 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu269 Eukaryota      Alveolata       Ciliophora         Spirotrichea
Otu270 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu271 Eukaryota       Hacrobia   Centroheliozoa     Centroheliozoa_X
Otu272 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu273 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu274 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu275 Eukaryota  Stramenopiles  Stramenopiles_X                 MOCH
Otu276 Eukaryota  Stramenopiles       Ochrophyta     Dictyochophyceae
Otu277 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu278 Eukaryota   Opisthokonta          Metazoa           Arthropoda
Otu279 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu280 Eukaryota  Stramenopiles       Ochrophyta      Bacillariophyta
Otu281 Eukaryota  Stramenopiles       Ochrophyta        Chrysophyceae
Otu282 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu283 Eukaryota Archaeplastida      Chlorophyta      Mamiellophyceae
Otu284 Eukaryota Archaeplastida     Streptophyta  Klebsormidiophyceae
Otu285 Eukaryota      Alveolata        Dinophyta          Dinophyceae
Otu286 Eukaryota       Hacrobia       Haptophyta     Prymnesiophyceae
Otu287 Eukaryota       Hacrobia      Cryptophyta        Cryptophyceae
                          Order                               Family
Otu001              Mamiellales                       Bathycoccaceae
Otu002       Prymnesiophyceae_X                  Braarudosphaeraceae
Otu003              Mamiellales                       Bathycoccaceae
Otu004            Dinophyceae_X                        Dinophyceae_X
Otu005             Mediophyceae                       Mediophyceae_X
Otu006        Bacillariophyceae                  Bacillariophyceae_X
Otu007          Pelagophyceae_X                      Pelagophyceae_X
Otu008            Dinophyceae_X                        Dinophyceae_X
Otu009             Prymnesiales                 Chrysochromulinaceae
Otu010               Craniata_X                          Craniata_XX
Otu011          Chrysophyceae_X                Chrysophyceae_Clade_C
Otu012            Dinophyceae_X                        Dinophyceae_X
Otu013    Syndiniales_Group_III              Syndiniales_Group_III_X
Otu014          Chrysophyceae_X                Chrysophyceae_Clade_G
Otu015            Dinophyceae_X                        Dinophyceae_X
Otu016             Pterocystida                       Pterocystida_X
Otu017          Agaricomycotina                       Agaricomycetes
Otu018       Dictyochophyceae_X                         Pedinellales
Otu019          Agaricomycotina                       Agaricomycetes
Otu020       Prymnesiophyceae_X                  Braarudosphaeraceae
Otu021            Dinophyceae_X                        Dinophyceae_X
Otu022       Prymnesiophyceae_X                   Prymnesiophyceae_X
Otu023        Bacillariophyceae                  Bacillariophyceae_X
Otu024    Klebsormidiophyceae_X               Klebsormidiophyceae_XX
Otu025              Mamiellales                         Mamiellaceae
Otu026        Bacillariophyceae                  Bacillariophyceae_X
Otu027               Suessiales                         Suessiales_X
Otu028           Isochrysidales                     Noelaerhabdaceae
Otu029         Saccharomycotina                    Saccharomycetales
Otu030          Cryptophyceae_X                      Cryptomonadales
Otu031      Syndiniales_Group_I          Syndiniales_Group_I_Clade_1
Otu032      Prasino_Clade_VII_X                  Prasino_Clade_VII_A
Otu033        Ulvales_relatives                  Ulvales_relatives_X
Otu034            Dinophyceae_X                        Dinophyceae_X
Otu035          Chrysophyceae_X                Chrysophyceae_Clade_G
Otu036          Haptophyta_HAP2                      Haptophyta_HAP2
Otu037        Bacillariophyceae                  Bacillariophyceae_X
Otu038          Chrysophyceae_X                Chrysophyceae_Clade_G
Otu039       Prymnesiophyceae_X                   Prymnesiophyceae_X
Otu040            Dinophyceae_X                        Dinophyceae_X
Otu041          Chrysophyceae_X                Chrysophyceae_Clade_I
Otu042            Dinophyceae_X                        Dinophyceae_X
Otu043          Haptophyta_HAP3                      Haptophyta_HAP3
Otu044              Mamiellales                         Mamiellaceae
Otu045                Borokales                           Borokaceae
Otu046                     <NA>                                 <NA>
Otu047       Dictyochophyceae_X                         Pedinellales
Otu048          Chrysophyceae_X                      Chrysophyceae_X
Otu049                   MOCH_2                             MOCH_2_X
Otu050          Chrysophyceae_X                Chrysophyceae_Clade_H
Otu051       Ustilaginomycotina                    Exobasidiomycetes
Otu052          Embryophyceae_X                     Embryophyceae_XX
Otu053          Chrysophyceae_X                Chrysophyceae_Clade_I
Otu054                   MOCH_5                             MOCH_5_X
Otu055             Prymnesiales                       Prymnesiales_X
Otu056            Dinophyceae_X                        Dinophyceae_X
Otu057          Embryophyceae_X                     Embryophyceae_XX
Otu058            Coccolithales                       Calcidiscaceae
Otu059        Bacillariophyceae                  Bacillariophyceae_X
Otu060        Dolichomastigales                    Crustomastigaceae
Otu061    Syndiniales_Group_III              Syndiniales_Group_III_X
Otu062        Pyramimonadales_X                   Pyramimonadales_XX
Otu063             Haptophyta_X                         Haptophyta_X
Otu064         Saccharomycotina                    Saccharomycetales
Otu065             Prymnesiales                Prymnesiales_Clade_B3
Otu066 Prymnesiophyceae_Clade_D           Prymnesiophyceae_Clade_D_X
Otu067             Prymnesiales                 Chrysochromulinaceae
Otu068            Dinophyceae_X                        Dinophyceae_X
Otu069             Prymnesiales                 Chrysochromulinaceae
Otu070        Bacillariophyceae                  Bacillariophyceae_X
Otu071             Mediophyceae                       Mediophyceae_X
Otu072             Prymnesiales                       Prymnesiales_X
Otu073          Pelagophyceae_X                      Pelagophyceae_X
Otu074             Mediophyceae                       Mediophyceae_X
Otu075        Bacillariophyceae                  Bacillariophyceae_X
Otu076          Chrysophyceae_X                Chrysophyceae_Clade_H
Otu077             Pterocystida                       Pterocystida_X
Otu078            Phaeocystales                       Phaeocystaceae
Otu079     Syndiniales_Group_II        Syndiniales_Group_II_Clade_16
Otu080             Mediophyceae                       Mediophyceae_X
Otu081        Bacillariophyceae                  Bacillariophyceae_X
Otu082             Acanthoecida               Stephanoecidae_Group_H
Otu083             Mediophyceae                       Mediophyceae_X
Otu084                   MOCH_2                             MOCH_2_X
Otu085              Mamiellales                         Mamiellaceae
Otu086          Chrysophyceae_X                Chrysophyceae_Clade_C
Otu087      Coscinodiscophyceae                Coscinodiscophyceae_X
Otu088          Pelagophyceae_X                      Pelagophyceae_X
Otu089             Mediophyceae                       Mediophyceae_X
Otu090        Bacillariophyceae                  Bacillariophyceae_X
Otu091        Bacillariophyta_X                    Bacillariophyta_X
Otu092        Pyramimonadales_X                   Pyramimonadales_XX
Otu093                   MOCH_5                             MOCH_5_X
Otu094       Calcihaptophycidae                   Calcihaptophycidae
Otu095             Prymnesiales                Prymnesiales_Clade_B4
Otu096            Dinophyceae_X                        Dinophyceae_X
Otu097       Prymnesiophyceae_X                   Prymnesiophyceae_X
Otu098       Dictyochophyceae_X                         Pedinellales
Otu099       Prymnesiophyceae_X                   Prymnesiophyceae_X
Otu100             Mediophyceae                       Mediophyceae_X
Otu101            Dinophyceae_X                        Dinophyceae_X
Otu102          Chrysophyceae_X                Chrysophyceae_Clade_C
Otu103             Prymnesiales                 Chrysochromulinaceae
Otu104            Phaeocystales                       Phaeocystaceae
Otu105       Dictyochophyceae_X                         Dictyochales
Otu106             Mediophyceae                       Mediophyceae_X
Otu107             Pterocystida                       Pterocystida_X
Otu108                     <NA>                                 <NA>
Otu109            Phaeocystales                       Phaeocystaceae
Otu110        Bacillariophyta_X                    Bacillariophyta_X
Otu111             Mediophyceae                       Mediophyceae_X
Otu112          Embryophyceae_X                     Embryophyceae_XX
Otu113       Dictyochophyceae_X                         Pedinellales
Otu114              Mamiellales                       Bathycoccaceae
Otu115            Dinophyceae_X                        Dinophyceae_X
Otu116     Syndiniales_Group_II Syndiniales_Group_II_Clade_10_and_11
Otu117          Chrysophyceae_X                Chrysophyceae_Clade_I
Otu118       Prymnesiophyceae_X                   Prymnesiophyceae_X
Otu119              Mamiellales                         Mamiellaceae
Otu120              Mamiellales                       Bathycoccaceae
Otu121      Coscinodiscophyceae                Coscinodiscophyceae_X
Otu122              Chelicerata                            Arachnida
Otu123              Mamiellales                       Bathycoccaceae
Otu124          Agaricomycotina                      Tremellomycetes
Otu125        Bacillariophyceae                  Bacillariophyceae_X
Otu126          Cryptophyceae_X                      Cryptomonadales
Otu127             Prymnesiales                        Prymnesiaceae
Otu128             Pterocystida                       Pterocystida_X
Otu129       Dictyochophyceae_X                      Florenciellales
Otu130            Dinophyceae_X                        Dinophyceae_X
Otu131             Mediophyceae                       Mediophyceae_X
Otu132            Echinamoebida                        Vermamoebidae
Otu133          Agaricomycotina                      Tremellomycetes
Otu134          Chrysophyceae_X                Chrysophyceae_Clade_I
Otu135 Prymnesiophyceae_Clade_E           Prymnesiophyceae_Clade_E_X
Otu136            Dinophyceae_X                        Dinophyceae_X
Otu137       Prymnesiophyceae_X                   Prymnesiophyceae_X
Otu138          Embryophyceae_X                     Embryophyceae_XX
Otu139           Isochrysidales                      Isochrysidaceae
Otu140                   MOCH_1                             MOCH_1_X
Otu141              Mamiellales                       Bathycoccaceae
Otu142             Mediophyceae                       Mediophyceae_X
Otu143          Stramenopiles_X                      Stramenopiles_X
Otu144        Dolichomastigales                   Dolichomastigaceae
Otu145             Pterocystida                       Pterocystida_X
Otu146             Prymnesiales                        Prymnesiaceae
Otu147                   MAST_3                              MAST_3D
Otu148            Phaeocystales                       Phaeocystaceae
Otu149                   MOCH_2                             MOCH_2_X
Otu150          Chrysophyceae_X                      Chrysophyceae_X
Otu151        Prasinococcales_X              Prasinococcales_Clade_B
Otu152          Chrysophyceae_X                Chrysophyceae_Clade_G
Otu153            Dinophyceae_X                        Dinophyceae_X
Otu154            Phaeocystales                       Phaeocystaceae
Otu155                Telonemia                    Telonemia_Group_2
Otu156              Mamiellales                       Bathycoccaceae
Otu157          Chrysophyceae_X                Chrysophyceae_Clade_H
Otu158        Bacillariophyceae                  Bacillariophyceae_X
Otu159                   MOCH_2                             MOCH_2_X
Otu160       Ustilaginomycotina                    Exobasidiomycetes
Otu161             Pterocystida                       Pterocystida_X
Otu162       Dictyochophyceae_X                         Pedinellales
Otu163                   MOCH_1                             MOCH_1_X
Otu164             Pterocystida                       Pterocystida_X
Otu165        Bacillariophyceae                  Bacillariophyceae_X
Otu166         Saccharomycotina                    Saccharomycetales
Otu167      Coscinodiscophyceae                Coscinodiscophyceae_X
Otu168             Chlorellales                       Chlorellales_X
Otu169             Pterocystida                       Pterocystida_X
Otu170                   MOCH_2                             MOCH_2_X
Otu171        Pyramimonadales_X                   Pyramimonadales_XX
Otu172     Syndiniales_Group_II        Syndiniales_Group_II_Clade_14
Otu173         Saccharomycotina                    Saccharomycetales
Otu174          Chrysophyceae_X                Chrysophyceae_Clade_G
Otu175        Bacillariophyta_X                    Bacillariophyta_X
Otu176                     <NA>                                 <NA>
Otu177                     <NA>                                 <NA>
Otu178             Mediophyceae                       Mediophyceae_X
Otu179             Ochrophyta_X                         Ochrophyta_X
Otu180             Prymnesiales                        Prymnesiaceae
Otu181          Chrysophyceae_X                Chrysophyceae_Clade_C
Otu182              Mamiellales                       Bathycoccaceae
Otu183          Chrysophyceae_X                Chrysophyceae_Clade_C
Otu184       Dictyochophyceae_X                      Florenciellales
Otu185              Mamiellales                       Bathycoccaceae
Otu186         Prasino_Clade_IX                   Prasino_Clade_IX_B
Otu187             Pterocystida                       Pterocystida_X
Otu188              Mamiellales                       Bathycoccaceae
Otu189          Chrysophyceae_X                Chrysophyceae_Clade_C
Otu190       Dictyochophyceae_X                      Florenciellales
Otu191           Chlorarachnida                     Chlorarachnida_X
Otu192    Klebsormidiophyceae_X               Klebsormidiophyceae_XX
Otu193                   MOCH_1                             MOCH_1_X
Otu194             Mediophyceae                       Mediophyceae_X
Otu195          Agaricomycotina                      Tremellomycetes
Otu196             Oligotrichia                        Strombidiidae
Otu197                   MOCH_1                             MOCH_1_X
Otu198        Chytridiomycotina                     Chytridiomycetes
Otu199                   MOCH_2                             MOCH_2_X
Otu200          Chrysophyceae_X                Chrysophyceae_Clade_C
Otu201       Dictyochophyceae_X                         Dictyochales
Otu202                   MOCH_5                             MOCH_5_X
Otu203          Agaricomycotina                       Agaricomycetes
Otu204       Bacillariophytceae                       Bacillariaceae
Otu205        Bacillariophyceae                  Bacillariophyceae_X
Otu206          Chrysophyceae_X                Chrysophyceae_Clade_G
Otu207             Mediophyceae                       Mediophyceae_X
Otu208                     <NA>                                 <NA>
Otu209              Mamiellales                       Bathycoccaceae
Otu210              Mamiellales                       Bathycoccaceae
Otu211              Mamiellales                         Mamiellaceae
Otu212    Klebsormidiophyceae_X               Klebsormidiophyceae_XX
Otu213                 Parmales                         Triparmaceae
Otu214          Agaricomycotina                       Agaricomycetes
Otu215      Prasino_Clade_VII_X                  Prasino_Clade_VII_B
Otu216            Dinophyceae_X                        Dinophyceae_X
Otu217          Chrysophyceae_X                Chrysophyceae_Clade_G
Otu218              Mamiellales                       Bathycoccaceae
Otu219              Mamiellales                       Bathycoccaceae
Otu220        Prasinococcales_X              Prasinococcales_Clade_B
Otu221                     <NA>                                 <NA>
Otu222              Mamiellales                       Bathycoccaceae
Otu223            Echinamoebida                        Vermamoebidae
Otu224          Agaricomycotina                       Agaricomycetes
Otu225                     <NA>                                 <NA>
Otu226      Coscinodiscophyceae                Coscinodiscophyceae_X
Otu227              Mamiellales                       Bathycoccaceae
Otu228              Mamiellales                       Bathycoccaceae
Otu229                   MOCH_1                             MOCH_1_X
Otu230              Mamiellales                       Bathycoccaceae
Otu231         Saccharomycotina                    Saccharomycetales
Otu232        Bacillariophyceae                  Bacillariophyceae_X
Otu233        Bacillariophyta_X                    Bacillariophyta_X
Otu234              Mamiellales                       Bathycoccaceae
Otu235              Mamiellales                         Mamiellaceae
Otu236          Cryptophyceae_X                      Cryptomonadales
Otu237              Mamiellales                       Bathycoccaceae
Otu238           Glissomonadida                           Allapsidae
Otu239              Chelicerata                            Arachnida
Otu240      Syndiniales_Group_I          Syndiniales_Group_I_Clade_1
Otu241             Mediophyceae                       Mediophyceae_X
Otu242              Mamiellales                       Bathycoccaceae
Otu243             Pterocystida                       Pterocystida_X
Otu244          Stramenopiles_X                      Stramenopiles_X
Otu245              Mamiellales                       Bathycoccaceae
Otu246                   MOCH_5                             MOCH_5_X
Otu247          Pelagophyceae_X                      Pelagophyceae_X
Otu248       Bacillariophytceae                       Bacillariaceae
Otu249              Mamiellales                         Mamiellaceae
Otu250       Dictyochophyceae_X                         Dictyochales
Otu251              Mamiellales                       Bathycoccaceae
Otu252                     <NA>                                 <NA>
Otu253              Mamiellales                       Bathycoccaceae
Otu254              Mamiellales                       Bathycoccaceae
Otu255        Bacillariophyta_X                    Bacillariophyta_X
Otu256                   MOCH_5                             MOCH_5_X
Otu257       Dictyochophyceae_X                         Pedinellales
Otu258             Pterocystida                       Pterocystida_X
Otu259          Cryptophyceae_X                      Cryptomonadales
Otu260        Bacillariophyta_X                    Bacillariophyta_X
Otu261             Pterocystida                       Pterocystida_X
Otu262             Pterocystida                       Pterocystida_X
Otu263            Dinophyceae_X                        Dinophyceae_X
Otu264             Pterocystida                       Pterocystida_X
Otu265                   MOCH_2                             MOCH_2_X
Otu266             Pterocystida                       Pterocystida_X
Otu267             Pterocystida                       Pterocystida_X
Otu268              Mamiellales                       Bathycoccaceae
Otu269            Choreotrichia                      Choreotrichia_X
Otu270             Pterocystida                       Pterocystida_X
Otu271             Pterocystida                       Pterocystida_X
Otu272              Mamiellales                         Mamiellaceae
Otu273              Mamiellales                         Mamiellaceae
Otu274       Prymnesiophyceae_X                  Braarudosphaeraceae
Otu275                   MOCH_5                             MOCH_5_X
Otu276       Dictyochophyceae_X                         Pedinellales
Otu277              Mamiellales                       Bathycoccaceae
Otu278              Chelicerata                            Arachnida
Otu279       Calcihaptophycidae                    Rhabdosphaeraceae
Otu280        Bacillariophyceae                  Bacillariophyceae_X
Otu281          Chrysophyceae_X                Chrysophyceae_Clade_C
Otu282              Mamiellales                       Bathycoccaceae
Otu283              Mamiellales                       Bathycoccaceae
Otu284    Klebsormidiophyceae_X               Klebsormidiophyceae_XX
Otu285            Dinophyceae_X                        Dinophyceae_X
Otu286           Isochrysidales                     Noelaerhabdaceae
Otu287          Cryptophyceae_X                      Cryptomonadales
                                        Genus
Otu001                           Ostreococcus
Otu002                           UCYN_A1_host
Otu003                            Bathycoccus
Otu004                           Prorocentrum
Otu005                          Thalassiosira
Otu006                       Pseudo_nitzschia
Otu007                            Pelagomonas
Otu008                          Dinophyceae_X
Otu009                       Chrysochromulina
Otu010               Craniata_XX_unclassified
Otu011                Chrysophyceae_Clade_C_X
Otu012                              Gonyaulax
Otu013                Syndiniales_Group_III_X
Otu014                Chrysophyceae_Clade_G_X
Otu015                          Dinophyceae_X
Otu016                         Pterocystida_X
Otu017                            Hyphodontia
Otu018                         Pedinellales_X
Otu019                            Itersonilia
Otu020                        Braarudosphaera
Otu021                          Dinophyceae_X
Otu022                          Syracosphaera
Otu023                    Bacillariophyceae_X
Otu024                          Klebsormidium
Otu025                             Micromonas
Otu026                          Cylindrotheca
Otu027                            Karlodinium
Otu028                              Emiliania
Otu029                           Debaryomyces
Otu030                              Teleaulax
Otu031          Syndiniales_Group_I_Clade_1_X
Otu032                Prasino_Clade_VII_A_4_X
Otu033                                   Ulva
Otu034                          Dinophyceae_X
Otu035                Chrysophyceae_Clade_G_X
Otu036                      Haptophyta_HAP2_X
Otu037                       Pseudo_nitzschia
Otu038                Chrysophyceae_Clade_G_X
Otu039                          Algirosphaera
Otu040                          Dinophyceae_X
Otu041                Chrysophyceae_Clade_I_X
Otu042                          Dinophyceae_X
Otu043                      Haptophyta_HAP3_X
Otu044                             Micromonas
Otu045                           Borokaceae_X
Otu046                        Chlorophyceae_X
Otu047                         Pedinellales_X
Otu048                        Chrysophyceae_X
Otu049                               MOCH_2_X
Otu050                Chrysophyceae_Clade_H_X
Otu051                             Malassezia
Otu052                                 Allium
Otu053                Chrysophyceae_Clade_I_X
Otu054                               MOCH_5_X
Otu055                         Prymnesiales_X
Otu056                          Dinophyceae_X
Otu057                                  Apium
Otu058                               Oolithus
Otu059                       Pseudo_nitzschia
Otu060                           Crustomastix
Otu061                Syndiniales_Group_III_X
Otu062                            Pyramimonas
Otu063                           Haptophyta_X
Otu064         Saccharomycetales_unclassified
Otu065                Prymnesiales_Clade_B3_X
Otu066             Prymnesiophyceae_Clade_D_X
Otu067                       Chrysochromulina
Otu068                          Dinophyceae_X
Otu069                       Chrysochromulina
Otu070                    Bacillariophyceae_X
Otu071                            Chaetoceros
Otu072                         Prymnesiales_X
Otu073                        Pelagophyceae_X
Otu074                          Thalassiosira
Otu075                              Nitzschia
Otu076                Chrysophyceae_Clade_H_X
Otu077                         Pterocystida_X
Otu078                            Phaeocystis
Otu079        Syndiniales_Group_II_Clade_16_X
Otu080                            Chaetoceros
Otu081                       Pseudo_nitzschia
Otu082               Stephanoecidae_Group_H_X
Otu083                               Eucampia
Otu084                               MOCH_2_X
Otu085                             Micromonas
Otu086                Chrysophyceae_Clade_C_X
Otu087                         Leptocylindrus
Otu088                            Aureococcus
Otu089                          Thalassiosira
Otu090                    Bacillariophyceae_X
Otu091                      Bacillariophyta_X
Otu092                            Pterosperma
Otu093                               MOCH_5_X
Otu094                   Calcihaptophycidae_X
Otu095                Prymnesiales_Clade_B4_X
Otu096                          Dinophyceae_X
Otu097            Syracosphaera/Algirosphaera
Otu098                         Pedinellales_X
Otu099                     Prymnesiophyceae_X
Otu100                         Mediophyceae_X
Otu101                          Dinophyceae_X
Otu102                Chrysophyceae_Clade_C_X
Otu103                       Chrysochromulina
Otu104                            Phaeocystis
Otu105                         Dictyochales_X
Otu106                         Mediophyceae_X
Otu107                         Pterocystida_X
Otu108                        Chlorophyceae_X
Otu109                            Phaeocystis
Otu110                      Bacillariophyta_X
Otu111                            Chaetoceros
Otu112                           Lycopersicon
Otu113                        Pseudopedinella
Otu114                           Ostreococcus
Otu115                          Dinophyceae_X
Otu116 Syndiniales_Group_II_Clade_10_and_11_X
Otu117                Chrysophyceae_Clade_I_X
Otu118                     Prymnesiophyceae_X
Otu119                            Mantoniella
Otu120                            Bathycoccus
Otu121                              Guinardia
Otu122                                Demodex
Otu123                           Ostreococcus
Otu124           Tremellomycetes_unclassified
Otu125                    Bacillariophyceae_X
Otu126                              Teleaulax
Otu127                             Prymnesium
Otu128                         Pterocystida_X
Otu129                           Florenciella
Otu130                          Dinophyceae_X
Otu131                          Thalassiosira
Otu132                             Vermamoeba
Otu133                           Filobasidium
Otu134                Chrysophyceae_Clade_I_X
Otu135             Prymnesiophyceae_Clade_E_X
Otu136                           Prorocentrum
Otu137                            Phaeocystis
Otu138                                 Citrus
Otu139                            Tisochrysis
Otu140                               MOCH_1_X
Otu141                           Ostreococcus
Otu142                         Mediophyceae_X
Otu143                        Stramenopiles_X
Otu144                          Dolichomastix
Otu145                         Pterocystida_X
Otu146                             Dicrateria
Otu147                              MAST_3D_X
Otu148                            Phaeocystis
Otu149                               MOCH_2_X
Otu150                        Chrysophyceae_X
Otu151                           Prasinoderma
Otu152                Chrysophyceae_Clade_G_X
Otu153                          Dinophyceae_X
Otu154                            Phaeocystis
Otu155                    Telonemia_Group_2_X
Otu156                            Bathycoccus
Otu157                Chrysophyceae_Clade_H_X
Otu158                       Pseudo_nitzschia
Otu159                               MOCH_2_X
Otu160                             Malassezia
Otu161                         Pterocystida_X
Otu162                        Helicopedinella
Otu163                               MOCH_1_X
Otu164                         Pterocystida_X
Otu165                       Pseudo_nitzschia
Otu166                          Hanseniaspora
Otu167                         Leptocylindrus
Otu168                            Picochlorum
Otu169                         Pterocystida_X
Otu170                               MOCH_2_X
Otu171                            Halosphaera
Otu172        Syndiniales_Group_II_Clade_14_X
Otu173                                Candida
Otu174                Chrysophyceae_Clade_G_X
Otu175                      Bacillariophyta_X
Otu176                        Chlorophyceae_X
Otu177                        Chlorophyceae_X
Otu178                          Thalassiosira
Otu179                           Ochrophyta_X
Otu180                             Prymnesium
Otu181                Chrysophyceae_Clade_C_X
Otu182                            Bathycoccus
Otu183                Chrysophyceae_Clade_C_X
Otu184                      Florenciellales_X
Otu185                            Bathycoccus
Otu186                   Prasino_Clade_IX_B_X
Otu187                         Pterocystida_X
Otu188                            Bathycoccus
Otu189                Chrysophyceae_Clade_C_X
Otu190                           Florenciella
Otu191                           Bigelowiella
Otu192                          Klebsormidium
Otu193                               MOCH_1_X
Otu194                         Mediophyceae_X
Otu195           Tremellomycetes_unclassified
Otu196                         Pseudotontonia
Otu197                               MOCH_1_X
Otu198                     Chytridiomycetes_X
Otu199                               MOCH_2_X
Otu200                Chrysophyceae_Clade_C_X
Otu201                         Dictyochales_X
Otu202                               MOCH_5_X
Otu203            Agaricomycetes_unclassified
Otu204                         Fragilariopsis
Otu205                       Pseudo_nitzschia
Otu206                Chrysophyceae_Clade_G_X
Otu207                            Chaetoceros
Otu208                        Chlorophyceae_X
Otu209                           Ostreococcus
Otu210                           Ostreococcus
Otu211                             Micromonas
Otu212                          Klebsormidium
Otu213                               Triparma
Otu214                              Lentinula
Otu215                Prasino_Clade_VII_B_1_X
Otu216                              Gonyaulax
Otu217                Chrysophyceae_Clade_G_X
Otu218                           Ostreococcus
Otu219                            Bathycoccus
Otu220              Prasinococcales_Clade_B_X
Otu221                        Chlorophyceae_X
Otu222                           Ostreococcus
Otu223                             Vermamoeba
Otu224                               Trametes
Otu225                        Chlorophyceae_X
Otu226                         Leptocylindrus
Otu227                            Bathycoccus
Otu228                           Ostreococcus
Otu229                               MOCH_1_X
Otu230                           Ostreococcus
Otu231                               Yarrowia
Otu232                       Pseudo_nitzschia
Otu233                      Bacillariophyta_X
Otu234                            Bathycoccus
Otu235                             Micromonas
Otu236                             Hemiselmis
Otu237                           Ostreococcus
Otu238                           Allapsidae_X
Otu239                                Demodex
Otu240          Syndiniales_Group_I_Clade_1_X
Otu241                         Mediophyceae_X
Otu242                            Bathycoccus
Otu243                         Pterocystida_X
Otu244                        Stramenopiles_X
Otu245                           Ostreococcus
Otu246                               MOCH_5_X
Otu247                            Aureococcus
Otu248                         Fragilariopsis
Otu249                             Micromonas
Otu250                         Dictyochales_X
Otu251                           Ostreococcus
Otu252                        Chlorophyceae_X
Otu253                            Bathycoccus
Otu254                            Bathycoccus
Otu255                      Bacillariophyta_X
Otu256                               MOCH_5_X
Otu257                         Pedinellales_X
Otu258                         Pterocystida_X
Otu259                              Teleaulax
Otu260                      Bacillariophyta_X
Otu261                         Pterocystida_X
Otu262                         Pterocystida_X
Otu263                          Dinophyceae_X
Otu264                         Pterocystida_X
Otu265                               MOCH_2_X
Otu266                         Pterocystida_X
Otu267                         Pterocystida_X
Otu268                            Bathycoccus
Otu269                        Choreotrichia_X
Otu270                         Pterocystida_X
Otu271                         Pterocystida_X
Otu272                             Micromonas
Otu273                             Micromonas
Otu274                           UCYN_A1_host
Otu275                               MOCH_5_X
Otu276                         Pedinellales_X
Otu277                           Ostreococcus
Otu278                             Tyrophagus
Otu279                          Algirosphaera
Otu280                       Pseudo_nitzschia
Otu281                Chrysophyceae_Clade_C_X
Otu282                           Ostreococcus
Otu283                            Bathycoccus
Otu284                          Klebsormidium
Otu285                          Dinophyceae_X
Otu286                              Emiliania
Otu287                              Teleaulax
In [ ]:
# definir los nombres de las filas de la columna samples

samples_df <- samples_df %>% 
  tibble::column_to_rownames("sample")
In [ ]:
# Transformar en matrices otu y tablas de tax (la tabla de muestra se puede dejar como marco de datos)

otu_mat <- as.matrix(otu_mat)
tax_mat <- as.matrix(tax_mat)
In [ ]:
# Transformar a objetos phyloseq
conflicts_prefer(MicrobiotaProcess::tax_table)
conflicts_prefer(phyloseq::tax_table)

OTU = otu_table(otu_mat, taxa_are_rows = TRUE)
OTU
TAX = tax_table(tax_mat)
TAX
samples = sample_data(samples_df)
samples
# manejamos en un solo ojbeto los datos anteriormente transformados
carbom <- phyloseq(OTU, TAX, samples)
carbom
[conflicted] Removing existing preference.
[conflicted] Will prefer MicrobiotaProcess::tax_table over any other package.
[conflicted] Removing existing preference.
[conflicted] Will prefer phyloseq::tax_table over any other package.
A otu_table: 287 x 55 of type dbl
X10nX10pX11nX11pX120nX120pX121nX121pX122nX122p...X7nX7pX9nX9ptri01ntri01ptri02ntri02ptri03ntri03p
Otu001136796292 42250018850 5 43 7138 943210541...12541 65164539453 0 27 49 4 30 3
Otu002 187134 389830 4561420 18223751 36 11...10010 161666 232719119746067 2827 5217261
Otu003 99398983 31 1324620 19 19 1612502 3831... 23 849338939 0 25 45 7 12 3
Otu004 36754234 24 22 11 1632967 35 6 18... 814922 6 12 5 0 3 0 3 8
Otu005 0 5 0 7 0 8 0 1620166 0... 15 0 2 0 0 0 0 0 0 13
Otu006 0 8 0 0 0 8 0 0 5 3... 0 0 0 0 0 0 0 8 0 0
Otu007 4587 518 4 386 8775 5 6 110214336 0... 9 3 17972 0 11 4 1 0 18
Otu008 1 8 24408 3 29 612355 0 0... 762 2 0 752 0 0 0 8 5412 8
Otu009 115 914 3 325 0 629 1 834 5 0... 1520 675 64 3 214476 5 0 0 695
Otu010 780 823810 12 3279 0 12 7 3027 0... 0 0 158601385 5 2 719278 9
Otu011 0 3 2 2 0 13 5 5 4 7... 0 0 17696 0 8 0 0 3 0
Otu012 0 0 0 6 0 0 0 16 3 0... 8 0 0 0 0 0 0 0 0 8
Otu013 63212471 2 0 12 3 0 0 420272... 2 12 893 4 0 0 4 1 0 0
Otu014 0 82 43304 1 1667 4 9233 13 3... 2637 0 1 5 5 5 6 5 2 8
Otu015 0 12 0 3 7 25 1 6 10 0... 3 01155 5 4 1 0 0 0 0
Otu016 1 0 0 9 5 0 0 14 0 0... 1 0 325 0 2 4 10 5 732443
Otu017 0 0 0 0 0 0 0 0 17 8... 10 15 0 0 0 0 0 0 0 0
Otu018 1 0 9 911 0 0 15 2702 6 4... 2104 7 1 0 0 1 1 0 13 0
Otu019 0 0 13 0 0 0 29 0 0 0... 0 0 0 0 0 0 0 0 7 0
Otu020 425 0 1 0 1706 0 8447 1 0 0... 1 1267 0 431 0 2191 0 0 0 0
Otu021 0 4 0 0 0 10 0 0 0 0... 0 0 3 0 1 0 0 9 0 0
Otu022 0 0 04987 0 0 0 6 90 1... 6 4 0 0 0 5 0 4 5 8
Otu023 4 0 1 0 0 3 0 0 0 0... 2053 0 0 0 0 1 2 0 2 399
Otu024 0 0 0 0 0 0 0 0 0 0... 0 0 0 8 0 9 0 0 0 0
Otu025 69 0 0 0 290 0 0 0 21 0... 0 0 0 0 0 0 3 0 6472 0
Otu026 0 2 0 0 0 3 0 0 0 1... 0 2 0 0 192 7767 213547 3 5
Otu027 62304 0 0 5 0 0 0 57 4... 0 1 0 7 0 12 6 0 0 0
Otu028 19 467 0 363 79 0 1 816 1 0... 91 1 02242 0 134924 0 2 5
Otu029 01271 0 1 0 0 1794 1 1762 929... 1 12 0 0 3 0 2 0 1 3
Otu030 0 5 0 0 0 4 0 0 155 0... 0 0 0 0 0 0 0 4 0 0
...............................................................
Otu2580000000 000...00000000014
Otu2590000000 010...000000000 0
Otu2600000000 000...000000000 0
Otu2610000000 000...00000000018
Otu2620000000 000...000000000 0
Otu2630000000 000...000000000 0
Otu2640000000 000...00000000014
Otu26500030001000...000000000 0
Otu2660000000 000...00000000012
Otu2670000000 000...000000000 0
Otu2680000200 010...000000000 0
Otu2690000000 000...000000000 0
Otu2700000000 100...00000000012
Otu2710000000 000...000000000 0
Otu2723000000 000...000000000 0
Otu2730000000 000...000000000 0
Otu2740000000 000...400000000 0
Otu2750000000 000...000000000 0
Otu2760000000 000...000000000 0
Otu2770000000 700...050000000 0
Otu2780000000 000...000000000 0
Otu2790000000 000...030000000 0
Otu2800000000 000...000000000 0
Otu2810000000 000...000000000 0
Otu2820000000 900...000000000 0
Otu2830100000 000...000000000 0
Otu2840000000 000...000000000 0
Otu2850000000 000...000000000 0
Otu2860000000 000...000000000 0
Otu2870000000 000...000000000 0
A taxonomyTable: 287 x 7 of type chr
DomainSupergroupDivisionClassOrderFamilyGenus
Otu001EukaryotaArchaeplastidaChlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Ostreococcus
Otu002EukaryotaHacrobia Haptophyta Prymnesiophyceae Prymnesiophyceae_X Braarudosphaeraceae UCYN_A1_host
Otu003EukaryotaArchaeplastidaChlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Bathycoccus
Otu004EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Prorocentrum
Otu005EukaryotaStramenopiles Ochrophyta Bacillariophyta Mediophyceae Mediophyceae_X Thalassiosira
Otu006EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyceae Bacillariophyceae_X Pseudo_nitzschia
Otu007EukaryotaStramenopiles Ochrophyta Pelagophyceae Pelagophyceae_X Pelagophyceae_X Pelagomonas
Otu008EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu009EukaryotaHacrobia Haptophyta Prymnesiophyceae Prymnesiales Chrysochromulinaceae Chrysochromulina
Otu010EukaryotaOpisthokonta Metazoa Craniata Craniata_X Craniata_XX Craniata_XX_unclassified
Otu011EukaryotaStramenopiles Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade_C Chrysophyceae_Clade_C_X
Otu012EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Gonyaulax
Otu013EukaryotaAlveolata Dinophyta Syndiniales Syndiniales_Group_IIISyndiniales_Group_III_XSyndiniales_Group_III_X
Otu014EukaryotaStramenopiles Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade_G Chrysophyceae_Clade_G_X
Otu015EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu016EukaryotaHacrobia CentroheliozoaCentroheliozoa_X Pterocystida Pterocystida_X Pterocystida_X
Otu017EukaryotaOpisthokonta Fungi Basidiomycota Agaricomycotina Agaricomycetes Hyphodontia
Otu018EukaryotaStramenopiles Ochrophyta Dictyochophyceae Dictyochophyceae_X Pedinellales Pedinellales_X
Otu019EukaryotaOpisthokonta Fungi Basidiomycota Agaricomycotina Agaricomycetes Itersonilia
Otu020EukaryotaHacrobia Haptophyta Prymnesiophyceae Prymnesiophyceae_X Braarudosphaeraceae Braarudosphaera
Otu021EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu022EukaryotaHacrobia Haptophyta Prymnesiophyceae Prymnesiophyceae_X Prymnesiophyceae_X Syracosphaera
Otu023EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyceae Bacillariophyceae_X Bacillariophyceae_X
Otu024EukaryotaArchaeplastidaStreptophyta KlebsormidiophyceaeKlebsormidiophyceae_XKlebsormidiophyceae_XX Klebsormidium
Otu025EukaryotaArchaeplastidaChlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas
Otu026EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyceae Bacillariophyceae_X Cylindrotheca
Otu027EukaryotaAlveolata Dinophyta Dinophyceae Suessiales Suessiales_X Karlodinium
Otu028EukaryotaHacrobia Haptophyta Prymnesiophyceae Isochrysidales Noelaerhabdaceae Emiliania
Otu029EukaryotaOpisthokonta Fungi Ascomycota Saccharomycotina Saccharomycetales Debaryomyces
Otu030EukaryotaHacrobia Cryptophyta Cryptophyceae Cryptophyceae_X Cryptomonadales Teleaulax
........................
Otu258EukaryotaHacrobia Centroheliozoa Centroheliozoa_X Pterocystida Pterocystida_X Pterocystida_X
Otu259EukaryotaHacrobia Cryptophyta Cryptophyceae Cryptophyceae_X Cryptomonadales Teleaulax
Otu260EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyta_X Bacillariophyta_X Bacillariophyta_X
Otu261EukaryotaHacrobia Centroheliozoa Centroheliozoa_X Pterocystida Pterocystida_X Pterocystida_X
Otu262EukaryotaHacrobia Centroheliozoa Centroheliozoa_X Pterocystida Pterocystida_X Pterocystida_X
Otu263EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu264EukaryotaHacrobia Centroheliozoa Centroheliozoa_X Pterocystida Pterocystida_X Pterocystida_X
Otu265EukaryotaStramenopiles Stramenopiles_XMOCH MOCH_2 MOCH_2_X MOCH_2_X
Otu266EukaryotaHacrobia Centroheliozoa Centroheliozoa_X Pterocystida Pterocystida_X Pterocystida_X
Otu267EukaryotaHacrobia Centroheliozoa Centroheliozoa_X Pterocystida Pterocystida_X Pterocystida_X
Otu268EukaryotaArchaeplastidaChlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Bathycoccus
Otu269EukaryotaAlveolata Ciliophora Spirotrichea Choreotrichia Choreotrichia_X Choreotrichia_X
Otu270EukaryotaHacrobia Centroheliozoa Centroheliozoa_X Pterocystida Pterocystida_X Pterocystida_X
Otu271EukaryotaHacrobia Centroheliozoa Centroheliozoa_X Pterocystida Pterocystida_X Pterocystida_X
Otu272EukaryotaArchaeplastidaChlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas
Otu273EukaryotaArchaeplastidaChlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas
Otu274EukaryotaHacrobia Haptophyta Prymnesiophyceae Prymnesiophyceae_X Braarudosphaeraceae UCYN_A1_host
Otu275EukaryotaStramenopiles Stramenopiles_XMOCH MOCH_5 MOCH_5_X MOCH_5_X
Otu276EukaryotaStramenopiles Ochrophyta Dictyochophyceae Dictyochophyceae_X Pedinellales Pedinellales_X
Otu277EukaryotaArchaeplastidaChlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Ostreococcus
Otu278EukaryotaOpisthokonta Metazoa Arthropoda Chelicerata Arachnida Tyrophagus
Otu279EukaryotaHacrobia Haptophyta Prymnesiophyceae Calcihaptophycidae Rhabdosphaeraceae Algirosphaera
Otu280EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyceae Bacillariophyceae_X Pseudo_nitzschia
Otu281EukaryotaStramenopiles Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade_C Chrysophyceae_Clade_C_X
Otu282EukaryotaArchaeplastidaChlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Ostreococcus
Otu283EukaryotaArchaeplastidaChlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Bathycoccus
Otu284EukaryotaArchaeplastidaStreptophyta KlebsormidiophyceaeKlebsormidiophyceae_XKlebsormidiophyceae_XXKlebsormidium
Otu285EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu286EukaryotaHacrobia Haptophyta Prymnesiophyceae Isochrysidales Noelaerhabdaceae Emiliania
Otu287EukaryotaHacrobia Cryptophyta Cryptophyceae Cryptophyceae_X Cryptomonadales Teleaulax
A sample_data: 55 x 28
fractionSelect_18S_nifHtotal_18Stotal_16Stotal_nifHsample_numbertransectstationdepthlatitude...phosphatessilicatesammonianitratesnitritestemperaturefluorescencesalinitysample_labelcosta
<chr><chr><dbl><dbl><dbl><chr><dbl><chr><dbl><dbl>...<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>
X10nNanoYes 53230 8772 3610 181 140-27.42...0.2 1.64 0 0.26 7.0000000000000007E-217.3553.7999999999999535.9 TR1_St81_140m_10n Sergipe
X10pPicoYes 47390 4448 624110 181 140-27.42...0.2 1.64 0 0.26 7.0000000000000007E-217.3553.7999999999999535.9 TR1_St81_140m_10p Sergipe
X11nNanoNo 24007 6193 377211 185 110-26.80...0.289999999999999981.58 0 0.22 0.05 21.3397.5 36.5 TR1_St85_110m_11n Esp<U+00ED>rito Santo
X11pPicoYes 31899 14 1020111 185 110-26.80...0.289999999999999981.58 0 0.22 0.05 21.3397.5 36.5 TR1_St85_110m_11p Esp<U+00ED>rito Santo
X120nNanoYes 70455 5292 93120 296 5-27.39...0.43 4 0 0.19 0.14000000000000001 23.1149.3000000000000133.5 TR2_St96_5m_120n Esp<U+00ED>rito Santo
X120pPicoYes 7618253272 23147120 296 5-27.39...0.43 4 0 0.19 0.14000000000000001 23.1149.3000000000000133.5 TR2_St96_5m_120p Esp<U+00ED>rito Santo
X121nNanoYes 52401 5958 26838121 296 30-27.39...0.43 3.89 0.040.23 0.09 22.6223.9 33.700000000000003TR2_St96_30m_121n Bah<U+00ED>a
X121pPicoYes 7178510993 23706121 296 30-27.39...0.43 3.89 0.040.23 0.09 22.6223.9 33.700000000000003TR2_St96_30m_121p Bah<U+00ED>a
X122nNanoYes 7874011730 15543122 296 50-27.39...0.560000000000000056.59 0.040.21 7.0000000000000007E-220.3779.6 35.9 TR2_St96_50m_122n R<U+00ED>o de Janeiro
X122pPicoYes 3736411817 11045122 296 50-27.39...0.560000000000000056.59 0.040.21 7.0000000000000007E-220.3779.6 35.9 TR2_St96_50m_122p R<U+00ED>o de Janeiro
X125nNanoYes 27381 9 14331125 298 5-27.59...0.289999999999999981.86 0.040.25 7.0000000000000007E-223.189.3 35.700000000000003TR2_St98_5m_125n R<U+00ED>o de Janeiro
X125pPicoYes 5517910419 21461125 298 5-27.59...0.289999999999999981.86 0.040.25 7.0000000000000007E-223.189.3 35.700000000000003TR2_St98_5m_125p R<U+00ED>o de Janeiro
X126nNanoYes 65714 15 16929126 298 50-27.59...0.25 0.98 0 0.2 0.12 23.7113.2 37.200000000000003TR2_St98_50m_126n R<U+00ED>o de Janeiro
X126pPicoYes 30406 3 10140126 298 50-27.59...0.25 0.98 0 0.2 0.12 23.7113.2 37.200000000000003TR2_St98_50m_126p R<U+00ED>o de Janeiro
X127nNanoYes 60610 9 11493127 298 85-27.59...0.25 1.03 0 0.47 0.26 22.9427.5 37 TR2_St98_85m_127n Bah<U+00ED>a
X13nNanoYes 46001 33 2131613 186 105-26.33...0.34 1.09000000000000010.040.15 0.26 20.9425.6 36.299999999999997TR1_St86_105m_13n Bah<U+00ED>a
X13pPicoYes 59626 7217 1195413 186 105-26.33...0.34 1.09000000000000010.040.15 0.26 20.9425.6 36.299999999999997TR1_St86_105m_13p Bah<U+00ED>a
X140nNanoYes 4812610428 25286140 2101 5-27.79...0.289999999999999981.2 0 0.140000000000000010.05 23.554 36.5 TR2_St101_5m_140n Bah<U+00ED>a
X140pPicoYes 4656910448 12301140 2101 5-27.79...0.289999999999999981.2 0 0.140000000000000010.05 23.554 36.5 TR2_St101_5m_140p Bah<U+00ED>a
X141nNanoYes 30081 6394 21302141 2101 60-27.79...0.25 1.03 0 0.22 0.09 23.7106.5 37.200000000000003TR2_St101_60m_141n Bah<U+00ED>a
X141pPicoYes 6422111318 10428141 2101 60-27.79...0.25 1.03 0 0.22 0.09 23.7106.5 37.200000000000003TR2_St101_60m_141p Bah<U+00ED>a
X142nNanoYes 8521923243 11753142 2101 110-27.79...0.289999999999999981.09000000000000010 0.84 0.23 23.3373 37.1 TR2_St101_110m_142n Bah<U+00ED>a
X142pPicoYes 89797 9553 17156142 2101 110-27.79...0.289999999999999981.09000000000000010 0.84 0.23 23.3373 37.1 TR2_St101_110m_142p Sergipe
X155nNanoYes 54162 8237 20674155 2106 5-28.12...0.25 1.03 0 0.37 0.09 23 55.3 36.9 TR2_St106_5m_155n Sergipe
X155pPicoYes 50782 7384 66172155 2106 5-28.12...0.25 1.03 0 0.37 0.09 23 55.3 36.9 TR2_St106_5m_155p Sergipe
X156nNanoYes 5506511371 14447156 2106 60-28.12...0.25 1.03 0 0.34 7.0000000000000007E-222.998.5 36.9 TR2_St106_60m_156n Sergipe
X156pPicoYes 43917 9665 16093156 2106 60-28.12...0.25 1.03 0 0.34 7.0000000000000007E-222.998.5 36.9 TR2_St106_60m_156p Sergipe
X157nNanoYes 29078 4978 15532157 2106 100-28.12...0.289999999999999980.98 0 0.4 7.0000000000000007E-221.5413.2 36.700000000000003TR2_St106_100m_157n Sergipe
X157pPicoYes 51848 9139 15204157 2106 100-28.12...0.289999999999999980.98 0 0.4 7.0000000000000007E-221.5413.2 36.700000000000003TR2_St106_100m_157p Sergipe
X15nNanoYes 22468 2887 267815 187 105-26.22...0.47 1.47 0 1.51 0.46 19.5473.7 36.1 TR1_St87_105m_15n Sergipe
X15pPicoYes 7839013813 103315 187 105-26.22...0.47 1.47 0 1.51 0.46 19.5473.7 36.1 TR1_St87_105m_15p R<U+00ED>o de Janeiro
X165nNanoYes 5073215337 14706165 2114 5-28.65...0.289999999999999981.36 0.090.280000000000000030.05 22.454.2 36.4 TR2_St114_5m_165n R<U+00ED>o de Janeiro
X165pPicoYes 4851410902 39918165 2114 5-28.65...0.289999999999999981.36 0.090.280000000000000030.05 22.454.2 36.4 TR2_St114_5m_165p R<U+00ED>o de Janeiro
X166nNanoYes 53412 3411 24442166 2114 60-28.65...0.16 0.98 0 0.25 7.0000000000000007E-221.475.90000000000000636.6 TR2_St114_60m_166n R<U+00ED>o de Janeiro
X166pPicoYes 6289712788 28107166 2114 60-28.65...0.16 0.98 0 0.25 7.0000000000000007E-221.475.90000000000000636.6 TR2_St114_60m_166p R<U+00ED>o de Janeiro
X167nNanoYes 3142412874 20616167 2114 80-28.65...0.2 0.98 0 0.21 0.02 21 242.9 36.6 TR2_St114_80m_167n R<U+00ED>o de Janeiro
X167pPicoYes 4993410885 13971167 2114 80-28.65...0.2 0.98 0 0.21 0.02 21 242.9 36.6 TR2_St114_80m_167p Bah<U+00ED>a
X1nNanoYes 95054 9139 1631 06 45-23.58...0.47 1.03 0 1.07 0.24 19.72773.75 36.299999999999997TR0_St6_45m_1n Bah<U+00ED>a
X1pPicoYes 19466159871371171 06 45-23.58...0.47 1.03 0 1.07 0.24 19.72773.75 36.299999999999997TR0_St6_45m_1p Bah<U+00ED>a
X2nNanoYes 4511110029 1432 06 45-23.58...0.47 1.03 0 1.07 0.24 19.72773.75 36.299999999999997TR0_St6_45m_2n Esp<U+00ED>rito Santo
X2pPicoYes107644145851138972 06 45-23.58...0.47 1.03 0 1.07 0.24 19.72773.75 36.299999999999997TR0_St6_45m_2p Esp<U+00ED>rito Santo
X3nNanoYes13103110037 1163 019 5-25.79...0.289999999999999981.31 0.040.48 0.02 22.737 36.9 TR0_St19_5m_3n Esp<U+00ED>rito Santo
X3pPicoYes134873 26 925003 019 5-25.79...0.289999999999999981.31 0.040.48 0.02 22.737 36.9 TR0_St19_5m_3p Esp<U+00ED>rito Santo
X5nNanoYes 24696 6340 773605 021 5-26.23...0.16 1.09000000000000010.150.9 0.05 22.898 36.9 TR0_St21_5m_5n Esp<U+00ED>rito Santo
X5pPicoYes11259016141 253415 021 5-26.23...0.16 1.09000000000000010.150.9 0.05 22.898 36.9 TR0_St21_5m_5p Esp<U+00ED>rito Santo
X7nNanoYes 40829 8443 76677 026 5-27.31...0.2 1.03 0.320.5 0.05 21.295.33 36.4 TR0_St26_5m_7n Esp<U+00ED>rito Santo
X7pPicoYes 22348 9254 269697 026 5-27.31...0.2 1.03 0.320.5 0.05 21.295.33 36.4 TR0_St26_5m_7p Esp<U+00ED>rito Santo
X9nNanoYes 19193 8156 349 181 140-27.42...0.2 1.64 0 0.26 7.0000000000000007E-217.3553.7999999999999535.9 TR1_St81_140m_9n Esp<U+00ED>rito Santo
X9pPicoYes 44610 29 539 181 140-27.42...0.2 1.64 0 0.26 7.0000000000000007E-217.3553.7999999999999535.9 TR1_St81_140m_9p Esp<U+00ED>rito Santo
tri01nNanoYes 1416211201 11792Trichod.12Bloom 0-27.80...NA NA NA NA NA NA NA NA TR2_StBloom_0m_tri01nEsp<U+00ED>rito Santo
tri01pPicoYes 3657614786 7772Trichod.12Bloom 0-27.80...NA NA NA NA NA NA NA NA TR2_StBloom_0m_tri01pEsp<U+00ED>rito Santo
tri02nNanoYes 2390614519 16934Trichod.22Bloom 0-27.80...NA NA NA NA NA NA NA NA TR2_StBloom_0m_tri02nSergipe
tri02pPicoYes 4688915320 17259Trichod.22Bloom 0-27.80...NA NA NA NA NA NA NA NA TR2_StBloom_0m_tri02pSergipe
tri03nNanoYes 34892 24 21523Trichod.32Bloom 0-27.80...NA NA NA NA NA NA NA NA TR2_StBloom_0m_tri03nSergipe
tri03pPicoYes 5563011558 15152Trichod.32Bloom 0-27.80...NA NA NA NA NA NA NA NA TR2_StBloom_0m_tri03 Sergipe
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 287 taxa and 55 samples ]
sample_data() Sample Data:       [ 55 samples by 28 sample variables ]
tax_table()   Taxonomy Table:    [ 287 taxa by 7 taxonomic ranks ]
In [ ]:
#Visualizar datos

sample_names(carbom)

rank_names(carbom)

sample_variables(carbom)
  1. 'X10n'
  2. 'X10p'
  3. 'X11n'
  4. 'X11p'
  5. 'X120n'
  6. 'X120p'
  7. 'X121n'
  8. 'X121p'
  9. 'X122n'
  10. 'X122p'
  11. 'X125n'
  12. 'X125p'
  13. 'X126n'
  14. 'X126p'
  15. 'X127n'
  16. 'X13n'
  17. 'X13p'
  18. 'X140n'
  19. 'X140p'
  20. 'X141n'
  21. 'X141p'
  22. 'X142n'
  23. 'X142p'
  24. 'X155n'
  25. 'X155p'
  26. 'X156n'
  27. 'X156p'
  28. 'X157n'
  29. 'X157p'
  30. 'X15n'
  31. 'X15p'
  32. 'X165n'
  33. 'X165p'
  34. 'X166n'
  35. 'X166p'
  36. 'X167n'
  37. 'X167p'
  38. 'X1n'
  39. 'X1p'
  40. 'X2n'
  41. 'X2p'
  42. 'X3n'
  43. 'X3p'
  44. 'X5n'
  45. 'X5p'
  46. 'X7n'
  47. 'X7p'
  48. 'X9n'
  49. 'X9p'
  50. 'tri01n'
  51. 'tri01p'
  52. 'tri02n'
  53. 'tri02p'
  54. 'tri03n'
  55. 'tri03p'
  1. 'Domain'
  2. 'Supergroup'
  3. 'Division'
  4. 'Class'
  5. 'Order'
  6. 'Family'
  7. 'Genus'
  1. 'fraction'
  2. 'Select_18S_nifH'
  3. 'total_18S'
  4. 'total_16S'
  5. 'total_nifH'
  6. 'sample_number'
  7. 'transect'
  8. 'station'
  9. 'depth'
  10. 'latitude'
  11. 'longitude'
  12. 'picoeuks'
  13. 'nanoeuks'
  14. 'bottom_depth'
  15. 'level'
  16. 'transect_distance'
  17. 'date'
  18. 'time'
  19. 'phosphates'
  20. 'silicates'
  21. 'ammonia'
  22. 'nitrates'
  23. 'nitrites'
  24. 'temperature'
  25. 'fluorescence'
  26. 'salinity'
  27. 'sample_label'
  28. 'costa'
In [ ]:
# vamos a conservar solo muestras para analizar (las que queremos analizar)

carbom <- subset_samples(carbom, Select_18S_nifH =="Yes")
carbom
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 287 taxa and 54 samples ]
sample_data() Sample Data:       [ 54 samples by 28 sample variables ]
tax_table()   Taxonomy Table:    [ 287 taxa by 7 taxonomic ranks ]
In [ ]:
# Mantenemos en este caso solo taxones fotosintéticos

carbom <- subset_taxa(carbom, Division %in% c("Chlorophyta", "Dinophyta", "Cryptophyta", 
                                              "Haptophyta", "Ochrophyta", "Cercozoa"))
carbom <- subset_taxa(carbom, !(Class %in% c("Syndiniales", "Sarcomonadea")))
carbom
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 205 taxa and 54 samples ]
sample_data() Sample Data:       [ 54 samples by 28 sample variables ]
tax_table()   Taxonomy Table:    [ 205 taxa by 7 taxonomic ranks ]
In [ ]:
# IMPORTANTE: Normalizar/escalar
# Normalizamos el número de lecturas en cada muestra utilizando la profundidad de secuenciación mediana.
# Normalizar en estadística se refiere a un proceso mediante el cual se ajustan los valores de una variable 
# para que estén en una escala común y comparable con otras variables. 
# En general, la normalización se utiliza para estandarizar los datos, de modo que las diferencias en la escala 
# o el rango de valores entre las diferentes variables no afecten el resultado de los análisis estadísticos.

# Algunos ejemplos comunes son la normalización z-score, la normalización min-max y la normalización por percentil

total = median(sample_sums(carbom))
total
standf = function(x, t=total) round(t * (x / sum(x)))
standf
carbom = transform_sample_counts(carbom, standf)
carbom
44903
function (x, t = total) 
round(t * (x/sum(x)))
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 205 taxa and 54 samples ]
sample_data() Sample Data:       [ 54 samples by 28 sample variables ]
tax_table()   Taxonomy Table:    [ 205 taxa by 7 taxonomic ranks ]
In [ ]:
# El número de lecturas utilizadas para la normalización es 44903 .

plot_bar(carbom, fill = "Division")

carbom
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 205 taxa and 54 samples ]
sample_data() Sample Data:       [ 54 samples by 28 sample variables ]
tax_table()   Taxonomy Table:    [ 205 taxa by 7 taxonomic ranks ]
No description has been provided for this image
In [ ]:
# lo mismo pero más bonito

plot_bar(carbom, fill = "Division") + 
  geom_bar(aes(color=Division, fill=Division), stat="identity", position="stack")
No description has been provided for this image
In [ ]:
# ahora para la Clase
plot_bar(carbom, fill = "Class")
carbom

plot_bar(carbom, fill = "Class") + 
  geom_bar(aes(color=Class, fill=Class), stat="identity", position="stack")
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 205 taxa and 54 samples ]
sample_data() Sample Data:       [ 54 samples by 28 sample variables ]
tax_table()   Taxonomy Table:    [ 205 taxa by 7 taxonomic ranks ]
No description has been provided for this image
No description has been provided for this image

PREVALENCIA/ABUNDANCIA¶

Lo primero que podemos mirar es la prevalencia de las features taxonómicas.

Primero que podemos hacer es crear un data frame con los valores de prevalencia, luego les agregamos la taxonomía y graficamos.

Computamos prevalencia para cada feature y la guardamos en un data frame

la prevalencia se refiere a la proporción de individuos en una población que tienen una enfermedad o condición específica en un momento dado. Por lo tanto, una prevalencia del 5% indica que el 5% de la población estudiada tiene la enfermedad o condición en cuestión en el momento en que se llevó a cabo el estudio.

In [ ]:
prevcarbom = apply(X = otu_table(carbom),
               MARGIN = ifelse(taxa_are_rows(carbom), yes = 1, no = 2),
               FUN = function(x){sum(x > 0)})
# Le agregamos la taxonomía
prevcarbom = data.frame(Prevalence = prevcarbom,
                    TotalAbundance = taxa_sums(carbom),
                    tax_table(carbom))

plyr::ddply(prevcarbom, "Division", function(df1){cbind(mean(df1$Prevalence),sum(df1$Prevalence))}) -> dfprevcarbom

# podemos ver en la consola la prevalencia
prevcarbom

#        Prevalence TotalAbundance    Domain     Supergroup    Division             Class
# Otu001         50         259644 Eukaryota Archaeplastida Chlorophyta   Mamiellophyceae
# Otu002         54         359480 Eukaryota       Hacrobia  Haptophyta  Prymnesiophyceae
# Otu003         52         279102 Eukaryota Archaeplastida Chlorophyta   Mamiellophyceae
A data.frame: 205 x 9
PrevalenceTotalAbundanceDomainSupergroupDivisionClassOrderFamilyGenus
<int><dbl><chr><chr><chr><chr><chr><chr><chr>
Otu00150259644EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Ostreococcus
Otu00254359480EukaryotaHacrobia Haptophyta Prymnesiophyceae Prymnesiophyceae_X Braarudosphaeraceae UCYN_A1_host
Otu00352279102EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Bathycoccus
Otu00450151580EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Prorocentrum
Otu00528 45560EukaryotaStramenopiles Ochrophyta Bacillariophyta Mediophyceae Mediophyceae_X Thalassiosira
Otu00622 47960EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyceae Bacillariophyceae_X Pseudo_nitzschia
Otu00742 84868EukaryotaStramenopiles Ochrophyta Pelagophyceae Pelagophyceae_X Pelagophyceae_X Pelagomonas
Otu00834 59937EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu00943 92316EukaryotaHacrobia Haptophyta Prymnesiophyceae Prymnesiales Chrysochromulinaceae Chrysochromulina
Otu01129 53322EukaryotaStramenopiles Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade_CChrysophyceae_Clade_C_X
Otu01218 48556EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Gonyaulax
Otu01441 54301EukaryotaStramenopiles Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade_GChrysophyceae_Clade_G_X
Otu01532 52928EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu01840 56796EukaryotaStramenopiles Ochrophyta Dictyochophyceae Dictyochophyceae_X Pedinellales Pedinellales_X
Otu02020 39708EukaryotaHacrobia Haptophyta Prymnesiophyceae Prymnesiophyceae_X Braarudosphaeraceae Braarudosphaera
Otu02119 14861EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu02233 37498EukaryotaHacrobia Haptophyta Prymnesiophyceae Prymnesiophyceae_X Prymnesiophyceae_X Syracosphaera
Otu02332 32811EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyceae Bacillariophyceae_X Bacillariophyceae_X
Otu02522 35716EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Mamiellaceae Micromonas
Otu02619 32017EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyceae Bacillariophyceae_X Cylindrotheca
Otu02721 23263EukaryotaAlveolata Dinophyta Dinophyceae Suessiales Suessiales_X Karlodinium
Otu02838 33453EukaryotaHacrobia Haptophyta Prymnesiophyceae Isochrysidales Noelaerhabdaceae Emiliania
Otu03022 24661EukaryotaHacrobia CryptophytaCryptophyceae Cryptophyceae_X Cryptomonadales Teleaulax
Otu03224 15784EukaryotaArchaeplastidaChlorophytaPrasino_Clade_VIIPrasino_Clade_VII_XPrasino_Clade_VII_A Prasino_Clade_VII_A_4_X
Otu03310 19643EukaryotaArchaeplastidaChlorophytaUlvophyceae Ulvales_relatives Ulvales_relatives_X Ulva
Otu03413 32984EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu03529 36098EukaryotaStramenopiles Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade_GChrysophyceae_Clade_G_X
Otu036 8 6566EukaryotaHacrobia Haptophyta Haptophyta_HAP2 Haptophyta_HAP2 Haptophyta_HAP2 Haptophyta_HAP2_X
Otu03711 9060EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyceae Bacillariophyceae_X Pseudo_nitzschia
Otu03823 23969EukaryotaStramenopiles Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade_GChrysophyceae_Clade_G_X
..............................
Otu241 322EukaryotaStramenopiles Ochrophyta Bacillariophyta Mediophyceae Mediophyceae_X Mediophyceae_X
Otu2421226EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Bathycoccus
Otu245 412EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Ostreococcus
Otu247 115EukaryotaStramenopiles Ochrophyta Pelagophyceae Pelagophyceae_X Pelagophyceae_X Aureococcus
Otu248 1 9EukaryotaStramenopiles Ochrophyta Bacillariophyta BacillariophytceaeBacillariaceae Fragilariopsis
Otu249 224EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Mamiellaceae Micromonas
Otu250 221EukaryotaStramenopiles Ochrophyta DictyochophyceaeDictyochophyceae_XDictyochales Dictyochales_X
Otu2511017EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Ostreococcus
Otu252 220EukaryotaArchaeplastidaChlorophytaChlorophyceae NA NA Chlorophyceae_X
Otu253 114EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Bathycoccus
Otu2541219EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Bathycoccus
Otu255 110EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyta_X Bacillariophyta_X Bacillariophyta_X
Otu257 528EukaryotaStramenopiles Ochrophyta DictyochophyceaeDictyochophyceae_XPedinellales Pedinellales_X
Otu259 321EukaryotaHacrobia CryptophytaCryptophyceae Cryptophyceae_X Cryptomonadales Teleaulax
Otu260 2 9EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyta_X Bacillariophyta_X Bacillariophyta_X
Otu263 1 9EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu268 814EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Bathycoccus
Otu272 336EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Mamiellaceae Micromonas
Otu273 240EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Mamiellaceae Micromonas
Otu274 213EukaryotaHacrobia Haptophyta PrymnesiophyceaePrymnesiophyceae_XBraarudosphaeraceae UCYN_A1_host
Otu276 110EukaryotaStramenopiles Ochrophyta DictyochophyceaeDictyochophyceae_XPedinellales Pedinellales_X
Otu277 216EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Ostreococcus
Otu279 213EukaryotaHacrobia Haptophyta PrymnesiophyceaeCalcihaptophycidaeRhabdosphaeraceae Algirosphaera
Otu280 2 4EukaryotaStramenopiles Ochrophyta Bacillariophyta Bacillariophyceae Bacillariophyceae_X Pseudo_nitzschia
Otu281 1 7EukaryotaStramenopiles Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade_CChrysophyceae_Clade_C_X
Otu282 2 7EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Ostreococcus
Otu283 6 9EukaryotaArchaeplastidaChlorophytaMamiellophyceae Mamiellales Bathycoccaceae Bathycoccus
Otu285 223EukaryotaAlveolata Dinophyta Dinophyceae Dinophyceae_X Dinophyceae_X Dinophyceae_X
Otu286 1 4EukaryotaHacrobia Haptophyta PrymnesiophyceaeIsochrysidales Noelaerhabdaceae Emiliania
Otu287 311EukaryotaHacrobia CryptophytaCryptophyceae Cryptophyceae_X Cryptomonadales Teleaulax
In [ ]:
# Otra forma de verlo (División) es de forma gráfica, asi:

prevcarbom1 = subset(prevcarbom, Division %in% get_taxa_unique(carbom, "Division"))
ggplot(prevcarbom1, aes(TotalAbundance, Prevalence / nsamples(carbom),color=Division)) +
  # Agregamos una línea para nuestro umbral
  geom_hline(yintercept = 0.05, alpha = 0.5, linetype = 2) +  geom_point(size = 2, alpha = 0.7) +
  scale_x_log10() +  xlab("Total Abundance") + ylab("Prevalence [Frac. Samples]") +
  facet_wrap(~Division) + theme(legend.position="none")
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In [ ]:
# en este caso la variamos con el Supergroup
prevcarbom2 = subset(prevcarbom, Supergroup %in% get_taxa_unique(carbom, "Supergroup"))
ggplot(prevcarbom2, aes(TotalAbundance, Prevalence / nsamples(carbom),color=Supergroup)) +
  # Agregamos una línea para nuestro umbral
  geom_hline(yintercept = 0.25, alpha = 0.5, linetype = 2) +  geom_point(size = 2, alpha = 0.7) +
  scale_x_log10() +  xlab("Total Abundance") + ylab("Prevalence [Frac. Samples]") +
  facet_wrap(~Supergroup) + theme(legend.position="none")
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In [ ]:
# Definimos el umbral de prevalencia a un 5%
(prevalenceThreshold = 0.05 * nsamples(carbom))

# [1] 2.7

keepTaxa = rownames(prevcarbom2)[(prevcarbom2$Prevalence >= prevalenceThreshold)]
(carbom2 = prune_taxa(keepTaxa, carbom))
2.7
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 143 taxa and 54 samples ]
sample_data() Sample Data:       [ 54 samples by 28 sample variables ]
tax_table()   Taxonomy Table:    [ 143 taxa by 7 taxonomic ranks ]

Y asi podriamos hacerlo con los datos que quisieramos. Si os fijais en el excel existe una columna llamada "fraction" con dos valores: Pico y Nano en el estudio, hace referencia a la composición de pico y nano-fitoplancton en el area Atlántico Sur frente a Brasil este analisis de clasificación se llevo a cabo por citometría de flujo

In [ ]:
# nosotros podemos realizar un analisis de composición de pico vs nano-fitoplancton, entonces reagrupamos muestras Pico vs Nano

carbom_fraction <- merge_samples(carbom, "fraction")
plot_bar(carbom_fraction, fill = "Division") + 
  geom_bar(aes(color=Division, fill=Division), stat="identity", position="stack")

# y vemos la abundancia de nano vs pico
Warning message in asMethod(object):
"NAs introducidos por coerci'on"
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"NAs introducidos por coerci'on"
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In [ ]:
# podemos tambien hacer paneles separados Pico vs Nano y Surface vs muestras Deep
carbom_chloro <- subset_taxa(carbom, Division %in% c("Chlorophyta"))
plot_bar(carbom_chloro, x="Division", fill = "Division", facet_grid = level~fraction) +
  geom_bar(aes(color=Genus, fill=Genus), stat="identity", position="stack")
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In [ ]:
# Division
carbom_chloro <- subset_taxa(carbom, Division %in% c("Chlorophyta"))
plot_bar(carbom_chloro, x="Genus", fill = "Genus", facet_grid = level~fraction) +
  geom_bar(aes(color=Genus, fill=Genus), stat="identity", position="stack")
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In [ ]:
set.seed(4235421)
# proj <- get_ordination(pseq, "MDS", "bray")
ord <- ordinate(carbom, "MDS", "bray")
In [ ]:
plot_ordination(carbom, ord, color = "fraction") +
                geom_point(size = 5)
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MAPAS DE CALOR/HEATMAP¶

NMDS son las siglas en inglés de Nonmetric Multidimensional Scaling, lo que en español se traduce como "Escalamiento Multidimensional No Métrico". Es una técnica estadística utilizada para visualizar y analizar datos de similitud o disimilitud entre objetos o individuos en el contexto de la metagenómica, se enfoca en el estudio del material genético presente en comunidades microbianas complejas.

In [ ]:
# en este caso el análisis NMDS de comunidades se baso en las principales OTU de ARNr 18S se realizó utilizando la distancia de Bray-Curtis 

plot_heatmap(carbom, method = "NMDS", distance = "bray")
Warning message:
"Transformation introduced infinite values in discrete y-axis"
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Está muy muy desordenado. Es mejor considerar solo las OTU más abundantes para los mapas de calor. Por ejemplo, solo se pueden tomar OTU que representen al menos el 20 % de las lecturas en al menos una muestra. Recordemos que normalizamos todas las muestras a la mediana del número de lecturas (total). Nos quedamos entonces solo con 33 OTUS lo que facilita mucho la lectura.

In [ ]:
carbom_abund <- filter_taxa(carbom, function(x) sum(x > total*0.20) > 0, TRUE)
carbom_abund

otu_table(carbom_abund)[1:8, 1:5]

plot_heatmap(carbom_abund, method = "NMDS", distance = "bray")
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 33 taxa and 54 samples ]
sample_data() Sample Data:       [ 54 samples by 28 sample variables ]
tax_table()   Taxonomy Table:    [ 33 taxa by 7 taxonomic ranks ]
A otu_table: 8 x 5 of type dbl
X10nX10pX11pX120nX120p
Otu00113339 7346 380412662 3
Otu002 18 832914958 3036206
Otu003 969210488 2016537 11
Otu004 3584 4943 33 7 9
Otu005 0 6 11 0 5
Otu006 0 9 0 0 5
Otu007 4473 605 587 5894 3
Otu008 1 9 6707 2 17
Warning message:
"Transformation introduced infinite values in discrete y-axis"
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In [ ]:
# otro ejemplo seria con esta metodologia: CCA/euclidean

plot_heatmap(carbom_chloro, method = "CCA", distance = "euclidean", 
             taxa.label = "Genus", taxa.order = "Genus", 
             low="beige", high="black", na.value="beige")
Warning message:
"Transformation introduced infinite values in discrete y-axis"
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In [ ]:
# Tambien es posible utilizar diferentes distancias y diferentes métodos multivariantes. 
# Por ejemplo, distancia Jaccard y MDS y etiquetar OTU con Clase, ordenar por Clase.
# También podemos cambiar la Paleta (la paleta por defecto es un poco fea…).

plot_heatmap(carbom_abund, method = "MDS", distance = "(A+B-2*J)/(A+B-J)", 
             taxa.label = "Class", taxa.order = "Class", 
             trans=NULL, low="beige", high="red", na.value="#04162c")

# tenemos opciones de utilizar muchas distancias integradas diferentes

dist_methods <- unlist(distanceMethodList)
print(dist_methods)
    UniFrac1     UniFrac2        DPCoA          JSD     vegdist1     vegdist2 
   "unifrac"   "wunifrac"      "dpcoa"        "jsd"  "manhattan"  "euclidean" 
    vegdist3     vegdist4     vegdist5     vegdist6     vegdist7     vegdist8 
  "canberra"       "bray" "kulczynski"    "jaccard"      "gower"   "altGower" 
    vegdist9    vegdist10    vegdist11    vegdist12    vegdist13    vegdist14 
  "morisita"       "horn"  "mountford"       "raup"   "binomial"       "chao" 
   vegdist15   betadiver1   betadiver2   betadiver3   betadiver4   betadiver5 
       "cao"          "w"         "-1"          "c"         "wb"          "r" 
  betadiver6   betadiver7   betadiver8   betadiver9  betadiver10  betadiver11 
         "I"          "e"          "t"         "me"          "j"        "sor" 
 betadiver12  betadiver13  betadiver14  betadiver15  betadiver16  betadiver17 
         "m"         "-2"         "co"         "cc"          "g"         "-3" 
 betadiver18  betadiver19  betadiver20  betadiver21  betadiver22  betadiver23 
         "l"         "19"         "hk"        "rlb"        "sim"         "gl" 
 betadiver24        dist1        dist2        dist3   designdist 
         "z"    "maximum"     "binary"  "minkowski"        "ANY" 
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También podemos construir nuestras propias distancias.

Para los vectores x e y, los términos "cuadráticos" son J = sum(x*y), A = sum(x^2), B = sum(y^2) y los términos "mínimos" son J = sum(pmin(x ,y)), A = sum(x) y B = sum(y), y los términos "binarios" son cualquiera de estos después de transformar los datos en forma binaria (número compartido de especies y número de especies para cada fila).

Algunos ejemplos:

A+B-2*J “cuadrático” euclidiano al cuadrado

A+B-2*J “mínimo” Manhattan

(A+B-2*J)/(A+B) “mínimo” Bray-Curtis

(A+B-2*J)/(A+B) “binario” Sørensen

A+B-2*J)/(A+BJ) Jaccard “binario”

Otra estrategia es hacer un mapa de calor para un grupo de taxonomía específico.

In [ ]:
# Por ejemplo, podemos apuntar a Chlorophyta y luego etiquetar las OTU usando el Género.

plot_heatmap(carbom_chloro, method = "NMDS", distance = "bray", 
             taxa.label = "Genus", taxa.order = "Genus", 
             low="beige", high="red", na.value="beige")
Warning message:
"Transformation introduced infinite values in discrete y-axis"
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Medidas de riqueza/rarefacción, uniformidad, dominancia, diversidad filogenética (diversidad alfa)¶

La rarefacción es un método utilizado en ecología para estandarizar la comparación de la diversidad de muestras con diferentes tamaños. Consiste en seleccionar una submuestra aleatoria del mismo tamaño (basado en la muestra más pequeña) de cada muestra y comparar los resultados. De esta manera, se estandariza la comparación y se evita que la diversidad de una muestra se vea afectada por el tamaño de la muestra.

DIVERSIDAD ALFA¶

Las medidas de diversidad alfa se utilizan para identificar la riqueza y uniformidad dentro de los taxones individuales. Las métricas/índices comúnmente utilizados son Shannon, Inverse Simpson, Simpson, Gini, Observed y Chao1. Estos índices no tienen en cuenta la filogenia de los taxones identificados en la secuenciación. La diversidad filogenética (PD de Faith) utiliza la distancia filogenética para calcular la diversidad de una muestra determinada.

Observad (simplemente el número de taxa o riqueza),

Chao1 (la riqueza ajustada por probabilidad de no observar especies),

ACE (riqueza que toma en cuenta la abundancia relativa),

Shannon (abundancia relativa de taxa),

Simpson (1 - la probabilidad de que observemos aleatoriamente dos bacterias en una comunidad y que pertenezcan a diferentes especies ),

Inverse Simpson ( 1 / Simpson),

Fisher (riqueza tomando en cuenta abundancia).

Es importante señalar que los índices de diversidad alfa son sensibles al ruido inherente a la aplicación de la reacción en cadena de la polimerasa y los errores de secuenciación.

Uno tiene que considerar la profundidad de secuenciación (cuántos taxones han sido muestreados) para cada muestra. Si hay una gran diferencia, entonces es importante normalizar las muestras a la misma profundidad de muestreo. Primero, observamos la profundidad de muestreo (cantidad de lecturas por muestra).

In [ ]:
# En phyloseq simplemente llamamos la función plot_richness y podemos visualizar las medidas de diversidad

# CON LOS ESTIMADORES OBSERVED, SHANON Y CHAO1
# aca lo hacemos con fraction (Pico-Nano) vs level (Sur-Deep)
plot_richness(carbom, color = "fraction", x= "level", measures = c("Observed", "Chao1", "Shannon")) + geom_boxplot(aes(fill = fraction), alpha=.7) + scale_color_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f")) + scale_fill_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f"))
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Las muestras Pico suelen ser menos diversas que las Nano cuando se observa la riqueza (Observed y Chao1), pero esta tendencia se invierte cuando se considera el índice de Shannon en el nivel.

Los puntos individuales fuera de las cajas representan outliers o valores atípicos, que son muestras con valores de diversidad mucho más altos o bajos que el resto en su grupo.

In [ ]:
# otro ejemplo
plot_richness(carbom, color = "Select_18S_nifH", x= "level", measures = c("Observed", "Chao1", "Shannon")) + geom_boxplot(aes(fill = Select_18S_nifH), alpha=.7) + scale_color_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f")) + scale_fill_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f"))
plot_richness(carbom, color = "Select_18S_nifH", x= "level", measures = c("ACE", "Chao1", "Fisher")) + geom_boxplot(aes(fill = Select_18S_nifH), alpha=.7) + scale_color_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f")) + scale_fill_manual(values = c("#a6cee3", "#b2df8a", "#fdbf6f"))
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In [ ]:
# Trazar estimador de riqueza Chao1 y estimador de diversidad de Shannon para todo carbom (otus)

plot_richness(carbom, measures=c("Chao1", "Shannon"))
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In [ ]:
# Reagrupar muestras de la misma fracción.

plot_richness(carbom, measures=c("Chao1", "Shannon"), x="level", color="fraction")
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DIVERSIDAD ENTRE ESPECIES BETA¶

En este ejercicio nos interesa comparar la diversidad entre divsiones

Recordemos que varias divisiones de organismos (ver tabla).

Necesitamos crear una lista de comparasiones de a pares para poder visualizar y calcular significancia estadística de manera simultánea.

En cuanto a diversidad beta podemos calcular similitud global a través de todas las muestras de interés o también podemos cuantificar la divergencia de un grupo y compararla con la divergencia de otro.

In [ ]:
# Veamos este caso primero.

# Calculamos las divergencias para la division Chlorophyta (subgrupo: Archaeplastida) y Dinophyta (subgrupo: Alveolata)

div.Archaeplastida <- divergence(subset_taxa(carbom, Division == "Chlorophyta"), apply(abundances(subset_taxa(carbom, Division == "Chlorophyta")), 1, median))
div.Alveolata <- divergence(subset_taxa(carbom, Division == "Dinophyta"), apply(abundances(subset_taxa(carbom, Division == "Dinophyta")), 1, median))

# transformamos el resultado anterior en _dataframes_
data.frame(div.Archaeplastida) -> df.div.Archaeplastida
data.frame(div.Alveolata) -> df.div.Alveolata

# Gather

df.div.Archaeplastida <- gather(df.div.Archaeplastida, taxa, divergence)
df.div.Alveolata <- gather(df.div.Alveolata, taxa, divergence)

# Agregamos columnas a nuestros _dataframes_

conflicts_prefer(ggpubr::mutate) # solución a problemas de conflicto
conflicts_prefer(ggpubr::mutate) # solución a problemas de conflicto

mutate(df.div.Archaeplastida, Division = "Archaeplastida") -> df.div.Archaeplastida
mutate(df.div.Alveolata, Division = "Alveolata") -> df.div.Alveolata

# Cambiamos los nombres de las columans de manera que sean iguales an ambos _dataframes_

colnames(df.div.Archaeplastida) <- c("taxa", "divergence", "Division")
colnames(df.div.Alveolata) <- c("taxa", "divergence", "Division")

# Los combinamos en un _dataframe_

rbind(df.div.Archaeplastida, df.div.Alveolata) -> div.boxplot

# Y finalmente graficamos y realizamos una comparación estadística

p2 <- ggboxplot(data = div.boxplot, x = "Division", y = "divergence", fill = "Division", palette = c("#a6cee3", "#fdbf6f"))
p2 + stat_compare_means(comparisons = list(c("Archaeplastida", "Alveolata")))
[conflicted] Removing existing preference.
[conflicted] Will prefer ggpubr::mutate over any other package.
[conflicted] Removing existing preference.
[conflicted] Will prefer ggpubr::mutate over any other package.
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Divergencia: La "divergencia" se refiere, en este contexto, a la variabilidad genética o diferencia en las secuencias de ADN/ARN de los organismos pertenecientes a las dos divisiones.

Comparación entre Divisiones:

Archaeplastida: Esta división tiene una mediana de divergencia más alta en comparación con Alveolata. También tiene varios valores atípicos en el rango inferior. Alveolata: Esta división tiene una mediana de divergencia ligeramente más baja y también presenta valores atípicos, pero en el rango superior. La cifra 0.023 entre las dos cajas sugiere que hay una diferencia estadísticamente significativa entre las medianas de las dos divisiones con un valor de p de 0.023. Esto significa que es probable que la diferencia observada entre las dos divisiones no se deba al azar.

Existen diferentes medidas de similitud (o disimilitud) disponibles que nos permiten entender las relaciones entre nuestras muestras.

En general todas producen matrices de distancia comparables.

El paquete phyloseq ofrece un gran número de medidas de distancia.

Las más populares son UniFrac y Weighted UniFrac (medidas que consideran filogenia) y otras independientes de filogenia como: Jaccard, Manhattan, Euclidian, Bray-Curtis, Canberra, etc.

In [ ]:
# ej independiente de filogenia.
# los datos de "costa" han sido inventados"

carbom.mds.bray <- ordinate(carbom, method = "MDS", distance = "bray")
evals <- carbom.mds.bray$values$Eigenvalues
pord1 <- plot_ordination(carbom, carbom.mds.bray, color = "costa") +
  labs(col = "costa") +
  coord_fixed(sqrt(evals[2] / evals[1]))
grid.arrange(pord1)
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ORDENACIÓN¶

In [ ]:
# análisis multivariable basado en la distancia de Bray-Curtis y la ordenación NMDS

carbom.ord <- ordinate(carbom, "NMDS", "bray")

# Trazamos OTU

plot_ordination(carbom, carbom.ord, type="taxa", color="Class", shape= "Division", 
                title="OTUs")
Square root transformation
Wisconsin double standardization
Run 0 stress 0.2317058 
Run 1 stress 0.244209 
Run 2 stress 0.2451212 
Run 3 stress 0.2626792 
Run 4 stress 0.2624512 
Run 5 stress 0.259957 
Run 6 stress 0.2503071 
Run 7 stress 0.2556401 
Run 8 stress 0.2488113 
Run 9 stress 0.2581377 
Run 10 stress 0.2302727 
... New best solution
... Procrustes: rmse 0.106655  max resid 0.3795624 
Run 11 stress 0.2650893 
Run 12 stress 0.2626179 
Run 13 stress 0.2456273 
Run 14 stress 0.2502234 
Run 15 stress 0.2510932 
Run 16 stress 0.2492831 
Run 17 stress 0.26479 
Run 18 stress 0.2506902 
Run 19 stress 0.2519276 
Run 20 stress 0.2487789 
*** Best solution was not repeated -- monoMDS stopping criteria:
    20: stress ratio > sratmax
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Un poco confuso, así que hacemos que sea más fácil de visualizar dividiéndolo según la división taxonómica.

In [ ]:
plot_ordination(carbom, carbom.ord, type="taxa", color="Class", 
                title="OTUs", label="Class") + 
  facet_wrap(~Division, 3)
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In [ ]:
# Ahora mostramos ejemplos y amplíamos los puntos para que sea más fácil de leer.

plot_ordination(carbom, carbom.ord, type="samples", color="fraction", 
                shape="level", title="Samples") + geom_point(size=3)
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In [ ]:
# ahora vemos  muestras y OTU pero en 2 paneles diferentes.

plot_ordination(carbom, carbom.ord, type="split", color="Class", 
                shape="level", title="biplot", label = "station") +  
  geom_point(size=3)
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ANALISIS DE REDES¶

Para finalizar, vamos a echar un vistazo a las capacidades de phyloseq para generar redes de co-occurrencia.

Las redes de co-ocurrencia nos dan pistas sobre potenciales interacciones ecológicas entre organismos.

Estas interacciones pueden ser directas o indirectas (no lo podemos determinar a partir de una red) y nos permiten comenzar a descifrar mecanismos ecológicos detrás de la composición de una comunidad microbiana.

En general en ecología tenemos distintos tipos de interacciones:

mutalismo, comensalismo, predación, amensalismo, competición o mutua depredación

Texto alternativo

Donde destacan depredación, competición o depredación mutua, y mutualismo.

Cada una de estas relaciones podría ser detectada en una red de co-ocurrencia según patrones de correlación positivos o negativos.

Veamos como generaríamos una red en phyloseq

In [ ]:
# Análisis de red simple

plot_net(carbom, distance = "(A+B-2*J)/(A+B)", type = "taxa", 
         maxdist = 0.8, color="Class", point_label="Genus")
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In [ ]:
# Esto es bastante confuso. Hagámoslo más simple usando solo OTU principales

plot_net(carbom, distance = "(A+B-2*J)/(A+B)", type = "taxa", 
         maxdist = 0.9, color="Class", point_label="Genus")

plot_net(carbom, type = "taxa", point_label = "Genus", 
         point_size = 10, point_alpha = 0.5, maxdist = 0.5, distance = "(A+B-2*J)/(A+B)", color= "Class", laymeth = "auto")
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In [ ]:
# parecido
plot_net(carbom, type = "taxa", point_label = "Genus", point_size = 10, point_alpha = 0.5, maxdist = 0.5, color = "Class", distance = "(A+B-2*J)/(A+B)", laymeth = "auto")
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IMPORTANTE!¶

La red generada con phyloseq no es una red de co-ocurrencia propiamente, es más bien una red que representa relaciones de distancia entre taxa o muestras. En nuestro ejemplo usamos muestras. Para una red de co-ocurrencia propiamente tal necesitamos usar las funciones del paquete: SpiecEasi

In [ ]:
library(SpiecEasi)

se.mb.psd4 <- spiec.easi(carbom, method = 'mb', lambda.min.ratio=1e-2,
                         nlambda=20, icov.select.params = list(rep.num=50))

# Obtener la matriz de adyacencia y convertirla a una matriz densa
adj_matrix <- getRefit(se.mb.psd4)
dense_adj_matrix <- as.matrix(adj_matrix)

# Crear el grafo usando la matriz densa
ig2.mb <- igraph::graph.adjacency(dense_adj_matrix, mode="undirected", weighted=TRUE, diag=FALSE)
V(ig2.mb)$name <- taxa_names(carbom)

plot_network(ig2.mb, carbom, type = "taxa", color = "Genus")
Applying data transformations...

Selecting model with pulsar using stars...

Fitting final estimate with mb...

done

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In [ ]:
se.glasso <- spiec.easi(carbom, method = 'mb', lambda.min.ratio=1e-2,
                         nlambda=20, icov.select.params = list(rep.num=50))
# Obtener la matriz de adyacencia y convertirla a una matriz densa
adj_matrix <- getRefit(se.mb.psd4)
dense_adj_matrix <- as.matrix(adj_matrix)

# Crear el grafo usando la matriz densa
ig2.mb <- igraph::graph.adjacency(dense_adj_matrix, mode="undirected", weighted=TRUE, diag=FALSE)
V(ig2.mb)$name <- taxa_names(carbom)

plot_network(ig2.mb, carbom, type = "taxa", color = "Supergroup")
Applying data transformations...

Selecting model with pulsar using stars...

Fitting final estimate with mb...

done

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Si se ven pocas conexiones en el gráfico, podría deberse a varias razones:

Interacciones Fuertes: spiec.easi busca interacciones fuertes y significativas en los datos. Si hay pocas conexiones, podría ser una indicación de que solo se han identificado pocas interacciones fuertes y confiables en tu conjunto de datos.

Parámetros del Modelo: La elección de parámetros para spiec.easi puede influir en el número de aristas identificadas. Por ejemplo, lambda.min.ratio y nlambda pueden ajustarse para identificar más o menos interacciones. Puede intentar ajustar estos parámetros para ver si obtiene más conexiones.